Simeon Jackson scored his 12th goal of the season to give Gillingham their first ever league success over Yeovil.
Jackson scored with a cheeky chip from the penalty spot after Febian Brandy had been brought down by Stefan Sam.
Manchester United loanee Brandy hit the bar and Alex McCarthy tipped Barry Fuller's 25-yard free-kick on to the post as the Gills pressed for a second.
But a miserable evening for Yeovil was compounded when Jean-Paul Kalala was sent off for a second bookable offence.
Gillingham manager Mark Stimson told BBC Radio Kent:
"It should have been more but we bumped into a very good goalkeeper.
"The boy Jackson (Simeon Jackson) came up with the quality again. Probably a few people might have been surprised he took it (the penalty) but it just shows you what the lad's got.
"Obviously Jacko (Jackson) felt confident and rightly so because he's scored a lot of good penalties for us and he took responsibility and put it away nicely."
Yeovil Town manager Terry Skiverton told BBC Somerset:
"We came out of the traps, and thought we were just going to turn up tonight, put the ball down, pass it and cause them problems.
"We came unstuck really early on. Their movement was good upfront, they were lively and we just didn't deal with it.
"There were a few disappointing incidents and referees have got to wise up to these kind of things."
90:00+4:48 The final whistle goes and the game is over.
90:00+4:28 Andy Barcham takes a short corner.
90:00+4:23 The ball is sent over by Andy Barcham, clearance by Danny Hutchins.
90:00+2:43 Free kick awarded for an unfair challenge on Gavin Tomlin by Curtis Weston. Centre by Ryan Mason, Header from close in by Stefan Stam misses to the right of the goal.
90:00+0:54 Curtis Weston restarts play with the free kick.
90:00+0:54 Substitution Febian Brandy leaves the field to be replaced by Dennis Oli.
90:00+0:54 Foul by Craig Alcock on Andy Barcham, free kick awarded.
89:59 The ball is crossed by Craig Alcock, clearance made by Simeon Jackson.
88:56 Matt Fry gives away a free kick for an unfair challenge on Gavin Tomlin. Free kick crossed right-footed by Shaun MacDonald, Kevin Maher makes a clearance.
87:05 The ball is delivered by Craig Alcock, Kevin Maher makes a clearance.
85:40 Ryan Mason has a shot on goal from outside the area which misses right.
82:05 Sam Williams gives away a free kick for an unfair challenge on Matt Fry. Simon Royce takes the direct free kick.
78:51 Chris Palmer takes the free kick.
78:51 Sent off Red card for JP Kalala.
78:45 JP Kalala challenges Kevin Maher unfairly and gives away a free kick.
77:42 Substitution Gavin Tomlin replaces Jonathan Obika.
75:34 Danny Hutchins challenges Curtis Weston unfairly and gives away a free kick. Free kick taken by Barry Fuller.
74:20 The ball is sent over by Ryan Mason, clearance made by Mark Bentley.
73:00 Outswinging corner taken right-footed by Ryan Mason, Mark Bentley manages to make a clearance.
72:49 Sam Williams takes a shot. Save made by Simon Royce.
72:18 Kevin Maher is penalised for handball and concedes a free kick. Free kick taken by Ryan Mason.
71:02 The free kick is swung in right-footed by Ryan Mason, free kick awarded for an unfair challenge on Mark Bentley by Stefan Stam. Free kick taken by Simon Royce.
71:02 Booking Febian Brandy receives a yellow card.
70:58 Booking The referee shows JP Kalala a yellow card.
70:29 Free kick awarded for a foul by Febian Brandy on JP Kalala.
68:30 Dean Bowditch sends in a cross, Matt Fry manages to make a clearance.
68:14 Simeon Jackson has an effort at goal from 12 yards. Save by Alex McCarthy.
67:27 Free kick taken by Kevin Maher.
67:27 Booking Booking for Dean Bowditch.
67:04 Dean Bowditch concedes a free kick for a foul on Barry Fuller.
65:43 Sam Williams is ruled offside. Josh Gowling restarts play with the free kick.
65:33 Febian Brandy crosses the ball, save by Alex McCarthy.
64:03 Free kick awarded for an unfair challenge on Josh Gowling by Sam Williams. Direct free kick taken by Barry Fuller.
62:33 Barry Fuller shoots direct from the free kick, save by Alex McCarthy.
62:33 Booking Stefan Stam booked.
62:21 Free kick awarded for an unfair challenge on Kevin Maher by JP Kalala.
62:10 The ball is crossed by Febian Brandy, Stefan Stam manages to make a clearance.
61:17 Chris Palmer crosses the ball, clearance made by Ryan Mason.
59:28 Substitution (Yeovil) makes a substitution, with Dean Bowditch coming on for Andrew Welsh.
57:39 Andrew Welsh takes a inswinging corner to the near post, Kevin Maher makes a clearance.
57:28 Effort from 25 yards by Ryan Mason. Blocked by Chris Palmer.
54:29 Craig Alcock produces a cross, save made by Simon Royce.
50:07 Corner taken right-footed by Ryan Mason from the left by-line to the near post, Kevin Maher makes a clearance.
49:20 Matt Fry gives away a free kick for an unfair challenge on Jonathan Obika. Free kick crossed left-footed by Andrew Welsh from right channel.
47:25 Unfair challenge on Shaun MacDonald by Kevin Maher results in a free kick. Free kick taken by Craig Alcock.
46:56 Chris Palmer produces a cross.
46:13 Outswinging corner taken left-footed by Chris Palmer, Febian Brandy takes a shot. Save by Alex McCarthy.
45:01 The referee starts the second half.
Half Time
45:00+1:39 The whistle is blown to end the first half.
45:00+1:03 Barry Fuller sends in a cross, clearance made by Shaun MacDonald.
45:00+0:37 Free kick awarded for an unfair challenge on Febian Brandy by Stefan Stam. Free kick taken by Kevin Maher.
44:45 Booking Booking for Josh Gowling for unsporting behaviour.
44:40 Booking Sam Williams booked.
42:22 Foul by Sam Williams on Josh Gowling, free kick awarded. Direct free kick taken by Simon Royce.
39:41 Barry Fuller gives away a free kick for an unfair challenge on Sam Williams. Ryan Mason fires a strike on goal direct from the free kick.
36:25 Corner taken by Chris Palmer, clearance by Danny Hutchins.
36:06 Unfair challenge on Kevin Maher by JP Kalala results in a free kick. Free kick taken by Kevin Maher.
35:08 The official flags Steven Caulker offside. Direct free kick taken by Simon Royce.
34:36 Foul by Curtis Weston on Shaun MacDonald, free kick awarded. Craig Alcock takes the free kick.
33:53 Sam Williams gives away a free kick for an unfair challenge on Josh Gowling. Simon Royce takes the direct free kick.
32:52 Shot by Ryan Mason. Josh Gowling gets a block in.
32:04 Inswinging corner taken by Andrew Welsh from the right by-line played to the near post, Kevin Maher makes a clearance.
30:01 Effort from outside the penalty area by Sam Williams goes wide left of the goal.
28:50 Febian Brandy has a drilled shot. Save by Alex McCarthy. Andy Barcham has an effort at goal. Fantastic save by Alex McCarthy.
28:09 Foul by Curtis Weston on Shaun MacDonald, free kick awarded. Danny Hutchins restarts play with the free kick.
27:07 The ball is crossed by Danny Hutchins, clearance made by Josh Gowling.
26:06 Andrew Welsh crosses the ball, clearance made by Josh Gowling.
24:47 The referee blows for offside. Free kick taken by Danny Hutchins.
23:25 Free kick taken by Barry Fuller.
23:25 Substitution (Yeovil) makes a substitution, with Sam Williams coming on for Scott Murray.
23:25 Ryan Mason concedes a free kick for a foul on Josh Gowling.
21:56 Corner taken right-footed by Chris Palmer, Effort on goal by Kevin Maher from 18 yards. Ryan Mason gets a block in. Andy Barcham produces a left-footed shot from the edge of the area and misses to the left of the target.
20:52 Febian Brandy takes a shot.
19:39 Outswinging corner taken by Chris Palmer from the right by-line, clearance made by Steven Caulker.
19:16 Andy Barcham takes the chance to get an effort at goal. Save by Alex McCarthy.
16:19 Corner taken short by Chris Palmer.
12:42 Effort from 12 yards by Simeon Jackson. Alex McCarthy makes a save.
12:26 Effort on goal by Craig Alcock from 20 yards. Matt Fry gets a block in.
10:26 Jonathan Obika is ruled offside. Simon Royce restarts play with the free kick.
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