Second-half goals from Bristol Rovers' Jo Kuffour and Chris Lines dealt a blow to Colchester's promotion hopes.
Dominic Blizzard's 25-yard shot put Rovers ahead, but Colchester levelled when John-Joe O'Toole deflected a Paul Ifil shot past Mikkel Andersen.
Kuffour forced the ball home from Lines' header after 67 minutes, and then provided the cross for Lines to make it 3-1 with an 80th-minute volley.
But Kayode Odejayi netted from 12 yards late on to set up a frantic finish.
Bristol Rovers manager Paul Trollope told BBC Radio Bristol:
"Chris Lines has got 10 goals now from midfield which is pleasing, and Jo Kuffour scored his first goal since Swindon which will give him a boost.
"We know as a group that when we get most people in the team and we're close to full fitness, we're a match for most teams in the division and certainly in the last two home games we've shown that."
Colchester United manager, Aidy Boothroyd told BBC Essex:
"Well, I can't remember being as annoyed as this.
"The atmosphere at the game was very quiet and they were expecting a real force. It was one of those games we should have been winning."
90:00+4:23 The referee brings the game to a close.
90:00+3:43 John-Joe O'Toole has an effort at goal from close range which goes wide of the left-hand upright.
90:00+2:58 John-Joe O'Toole delivers the ball, clearance made by Chris Lines.
90:00+2:34 Matt Heath takes a shot. Save by Mikkel Andersen.
90:00+0:37 Anthony Wordsworth takes a inswinging corner from the right by-line to the near post, clearance made by Stuart Campbell.
90:00+0:32 Ashley Vincent crosses the ball, clearance by Stuart Campbell.
88:54 Assist by Clive Platt.
88:54 GOAL - Kayode Odejayi:Bristol Rovers 3 - 2 Colchester Kayode Odejayi finds the net with a goal from inside the penalty area to the top right corner of the goal. Bristol Rovers 3-2 Colchester.
87:50 Ben Williams takes the free kick.
87:50 Substitution Kevin Lisbie replaces Danny Batth.
87:50 Substitution (Bristol Rovers) makes a substitution, with Ben Swallow coming on for Jeff Hughes.
87:50 Andrew Williams concedes a free kick for a foul on Marc Tierney.
86:29 Ashley Vincent is caught offside. Mikkel Andersen restarts play with the free kick.
85:41 Mikkel Andersen takes the free kick.
85:41 Substitution (Bristol Rovers) makes a substitution, with Carl Regan coming on for Dominic Blizzard.
85:41 The assistant referee flags for offside against Kayode Odejayi.
85:14 Anthony Wordsworth decides to take the corner short, Ashley Vincent sends in a cross.
85:05 Marc Tierney crosses the ball, save made by Mikkel Andersen.
83:31 John-Joe O'Toole produces a cross, free kick awarded for a foul by Anthony Wordsworth on Danny Coles. Direct free kick taken by Mikkel Andersen.
83:24 The ball is delivered by John-Joe O'Toole, clearance by Danny Coles.
82:54 Effort from the edge of the area by Andrew Williams goes wide of the left-hand post.
81:39 Inswinging corner taken by Anthony Wordsworth from the right by-line, Matt Heath takes a shot from close range clearing the crossbar.
81:17 David Prutton takes the inswinging corner, clearance made by Byron Anthony.
81:11 Anthony Wordsworth crosses the ball, blocked by Byron Anthony.
80:16 Outswinging corner taken left-footed by Daniel Jones from the left by-line, Matt Heath manages to make a clearance.
80:12 The ball is delivered by Daniel Jones, Danny Batth makes a clearance.
79:16 Substitution Andrew Williams comes on in place of Paul Heffernan.
78:26 Assist by Jo Kuffour.
78:26 GOAL - Chris Lines:Bristol Rovers 3 - 1 Colchester Chris Lines finds the net with a goal from close range low into the middle of the goal. Bristol Rovers 3-1 Colchester.
Correction - 76:34 Chris Lines delivers the ball from the free kick right-footed from right channel.
76:34 The free kick is swung in right-footed by Chris Lines, Matt Heath makes a clearance.
76:34 Booking The referee shows Marc Tierney a yellow card.
Correction - 76:22 Marc Tierney gives away a free kick for an unfair challenge on Dominic Blizzard.
76:22 Marc Tierney challenges Dominic Blizzard unfairly and gives away a free kick.
75:05 John White sends in a cross, free kick awarded for an unfair challenge on Mikkel Andersen by John-Joe O'Toole. Mikkel Andersen takes the free kick.
74:12 John White crosses the ball, clearance by Daniel Jones.
74:07 Ashley Vincent produces a cross, blocked by Jeff Hughes.
73:35 Daniel Jones concedes a free kick for a foul on Kayode Odejayi. Direct free kick taken by Ashley Vincent.
73:05 Byron Anthony produces a cross.
70:30 Substitution Philip Ifil leaves the field to be replaced by Ashley Vincent.
70:30 Substitution Steven Gillespie goes off and Kayode Odejayi comes on.
69:14 Philip Ifil takes a shot. Save by Mikkel Andersen.
67:55 Clive Platt takes a shot. Mikkel Andersen gets a block in.
66:55 Assist by Daniel Jones.
66:55 GOAL - Jo Kuffour:Bristol Rovers 2 - 1 Colchester A goal is scored by Jo Kuffour from inside the six-yard box low into the middle of the goal. Bristol Rovers 2-1 Colchester.
66:18 Daniel Jones takes the free kick.
66:18 Booking Philip Ifil receives a yellow card for unsporting behaviour.
66:12 Free kick awarded for a foul by Philip Ifil on Daniel Jones.
65:21 Unfair challenge on Stuart Campbell by Steven Gillespie results in a free kick. The free kick is swung in left-footed by Daniel Jones, Clive Platt manages to make a clearance.
65:04 A cross is delivered by Daniel Jones, Danny Batth manages to make a clearance.
63:59 Stuart Campbell has an effort at goal from just outside the box which goes wide of the left-hand post.
63:28 The ball is crossed by Jo Kuffour, clearance by John White.
60:25 Jeff Hughes delivers the ball, save by Ben Williams.
59:36 David Prutton crosses the ball, Byron Anthony makes a clearance.
59:10 Corner from the right by-line taken by Anthony Wordsworth, clearance by Danny Coles.
59:04 Centre by Marc Tierney, Steve Elliott manages to make a clearance.
57:17 John White takes the direct free kick.
57:17 Booking Steve Elliott is cautioned by the ref for unsporting behaviour.
57:07 Foul by Steve Elliott on Steven Gillespie, free kick awarded.
54:34 A cross is delivered by Matt Heath, clearance made by Chris Lines.
54:03 Inswinging corner taken by Anthony Wordsworth, clearance by Danny Coles.
53:57 The ball is delivered by Philip Ifil, Steve Elliott manages to make a clearance.
52:18 The ball is sent over by John White, Mikkel Andersen makes a save.
Correction - 51:40 Stuart Campbell produces a right-footed shot from just outside the box that goes wide right of the goal.
51:40 Stuart Campbell produces a right-footed shot from just outside the box that misses to the right of the target.
51:02 Centre by John White, Danny Coles makes a clearance.
47:37 Steven Gillespie is caught offside. Mikkel Andersen takes the indirect free kick.
45:01 The second half has started.
Half Time
45:00+2:14 The referee calls an end to the first half.
45:00+1:47 Effort from deep inside the area by Steven Gillespie misses to the left of the goal.
Correction - 42:31 Shot from long range by Steve Elliott goes wide of the left-hand upright.
42:31 Shot from long range by Steve Elliott goes wide of the left-hand post.
41:41 Steven Gillespie gives away a free kick for an unfair challenge on Steve Elliott. Byron Anthony restarts play with the free kick.
41:27 The ball is delivered by Byron Anthony, John White makes a clearance.
40:03 Paul Heffernan produces a drilled left-footed shot from deep inside the penalty box which goes wide of the right-hand upright.
39:03 John-Joe O'Toole challenges Chris Lines unfairly and gives away a free kick. Direct free kick taken by Mikkel Andersen.
37:08 Centre by Dominic Blizzard, clearance made by Danny Batth.
35:34 The official flags Steven Gillespie offside. Free kick taken by Mikkel Andersen.
34:40 Steven Gillespie takes a shot. Save made by Mikkel Andersen.
33:44 Clive Platt sends in a cross, clearance by Byron Anthony.
32:30 Jeff Hughes concedes a free kick for a foul on John White. Direct free kick taken by Ben Williams.
31:38 Shot by David Prutton from just outside the area goes over the net.
31:10 Jeff Hughes is penalised for handball and concedes a free kick. John White restarts play with the free kick.
29:25 The ball is sent over by Daniel Jones, clearance by John-Joe O'Toole. Outswinging corner taken left-footed by Daniel Jones from the left by-line, Clive Platt manages to make a clearance.
28:02 The referee gives a free kick against Steven Gillespie for handball. Free kick taken by Steve Elliott.
27:23 Daniel Jones challenges Philip Ifil unfairly and gives away a free kick. Ben Williams restarts play with the free kick.
27:14 Jeff Hughes sends in a cross, clearance by John White.
26:27 A cross is delivered by Byron Anthony, Marc Tierney gets a block in.
24:34 Stuart Campbell fouled by Steven Gillespie, the ref awards a free kick. Free kick crossed by Stuart Campbell, Steve Elliott concedes a free kick for a foul on Clive Platt. Ben Williams restarts play with the free kick.
24:23 A cross is delivered by Jeff Hughes, Matt Heath makes a clearance.
23:31 Free kick awarded for an unfair challenge on Jeff Hughes by Danny Batth. Stuart Campbell crosses the ball from the free kick right-footed from right channel, Matt Heath makes a clearance.
23:31 Booking The referee shows Danny Batth a yellow card.
21:31 Steven Gillespie fouled by Danny Coles, the ref awards a free kick. The free kick is delivered right-footed by David Prutton from left wing.
20:16 Assist by Philip Ifil.
20:16 GOAL - John-Joe O'Toole:Bristol Rovers 1 - 1 Colchester John-Joe O'Toole finds the back of the net with a headed goal from deep inside the penalty box. Bristol Rovers 1-1 Colchester.
20:07 Marc Tierney delivers the ball, clearance by Daniel Jones.
17:07 John White concedes a free kick for a foul on Jo Kuffour. Danny Coles takes the free kick.
15:34 Assist by Jeff Hughes.
15:34 GOAL - Dominic Blizzard:Bristol Rovers 1 - 0 Colchester Dominic Blizzard fires in a goal from outside the penalty area to the bottom right corner of the goal. Bristol Rovers 1-0 Colchester.
15:00 Steven Gillespie is flagged offside by the assistant referee. Free kick taken by Mikkel Andersen.
14:32 Free kick awarded for a foul by Philip Ifil on Steve Elliott. Stuart Campbell restarts play with the free kick.
14:26 The ball is delivered by Marc Tierney, clearance made by Danny Coles.
13:24 Philip Ifil fouled by Daniel Jones, the ref awards a free kick. John White crosses the ball in from the free kick, save by Mikkel Andersen.
12:41 The ball is delivered by David Prutton, Chris Lines makes a clearance.
11:24 The ball is sent over by Anthony Wordsworth, Steven Gillespie produces a right-footed shot from close range which goes wide of the left-hand post.
11:14 Philip Ifil delivers the ball, Daniel Jones gets a block in.
10:25 A cross is delivered by Matt Heath.
9:38 A cross is delivered by Marc Tierney, clearance made by Daniel Jones.
8:51 Anthony Wordsworth fouled by Dominic Blizzard, the ref awards a free kick. Ben Williams restarts play with the free kick.
8:05 Unfair challenge on Marc Tierney by Jo Kuffour results in a free kick. Free kick taken by Ben Williams.
7:57 The ball is crossed by Daniel Jones, clearance by Marc Tierney.
7:32 David Prutton produces a cross, save by Mikkel Andersen.
5:49 Unfair challenge on Byron Anthony by Anthony Wordsworth results in a free kick. Direct free kick taken by Byron Anthony.
5:49 Booking Anthony Wordsworth shown a yellow card.
5:16 Corner taken by David Prutton played to the near post, Steve Elliott manages to make a clearance.
4:20 Philip Ifil delivers the ball, Steven Gillespie takes a shot. Blocked by Mikkel Andersen.
3:29 David Prutton produces a left-footed shot from just outside the box that misses to the right of the net.
2:40 John-Joe O'Toole fouled by Paul Heffernan, the ref awards a free kick. Matt Heath restarts play with the free kick.
0:44 Paul Heffernan has shot on goal from just outside the penalty box which goes wide of the right-hand upright.
0:20 Anthony Wordsworth gives away a free kick for an unfair challenge on Dominic Blizzard. Direct free kick taken by Byron Anthony.
0:00 The referee gets the game started.
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