Scott McGleish scored in each half as Orient edged out Tranmere to secure a first win in seven games and gain revenge for their midweek FA Cup exit.
The O's went ahead when Andros Townsend and Ryan Jarvis combined to tee up McGleish who fired the ball home.
Rovers levelled through Charlie Bennett who scored on the rebound after keeper Glenn Morris saved John Welsh's shot.
But McGleish's near-post header from Sean Thornton's cross ensured maximum points for the home side.
Tranmere caretaker manager Les Parry told BBC Radio Merseyside:
"Towards the end of the first half we were praying he [the referee] wouldn't blow the whistle as we fancied ourselves getting a second goal.
"We had some good chances we didn't take. In the second half we came out and for some reason we didn't do what made us so much better in the first half."
Leyton Orient striker Scott McGleish told BBC London 94.9:
"We played really well, we got the ball down, we passed it like we've tried to do all year.
"It might not have looked like that, but that's what we want to do and that's the manager's philosophy.
"A cup run would have been nice for the club and the fans but as always, we want to move up in the league and today we've done that."
71:08 Ash Taylor fouled by Adrian Patulea, the ref awards a free kick. Luke Daniels takes the direct free kick.
70:35 The ball is crossed by Sean Thornton,
69:56 Sean Thornton provided the assist for the goal.
69:56 GOAL - Scott McGleish:Leyton Orient 2 - 1 Tranmere Scott McGleish gets on the score sheet with a goal from close range to the bottom right corner of the goal. Leyton Orient 2-1 Tranmere.
69:25 Corner from right by-line taken by Luke Summerfield.
68:56 Zoumana Bakayogo produces a cross, clearance by Charlie Daniels.
67:41 Zoumana Bakayogo concedes a free kick for a foul on Jimmy Smith. Andros Townsend restarts play with the free kick.
66:56 The ball is swung over by Stephen Purches, Marlon Broomes manages to make a clearance.
65:31 Glenn Morris takes the direct free kick.
65:31 Booking Ash Taylor receives a caution.
65:22 Ash Taylor concedes a free kick for a foul on Scott McGleish.
63:21 The assistant referee signals for offside against Craig Curran. Glenn Morris takes the free kick.
62:51 Chris Shuker takes a short corner.
60:54 Substitution Adrian Patulea joins the action as a substitute, replacing Ryan Jarvis.
60:18 The ball is sent over by Aaron Cresswell.
57:35 The ball is crossed by Andros Townsend.
55:51 Corner from left by-line taken by Chris Shuker.
54:54 Andros Townsend sends in a cross.
54:20 Sean Thornton produces a cross, clearance made by Aaron Cresswell. Corner taken by Sean Thornton from the left by-line to the near post.
53:29 Foul by Jimmy Smith on Craig Curran, free kick awarded. Chris Shuker delivers the ball from the free kick right-footed from left wing, clearance made by Jimmy Smith.
52:36 The referee blows for offside. Luke Daniels takes the direct free kick.
52:04 The official flags Jimmy Smith offside. Luke Daniels takes the free kick.
48:13 John Welsh takes a shot. Save by Glenn Morris.
45:01 The second half begins.
Half Time
45:00+2:20 The match has reached half-time.
45:00+1:17 Free kick awarded for an unfair challenge on Ryan Jarvis by Zoumana Bakayogo. Direct free kick taken by Andros Townsend.
45:00+0:39 Effort on goal by Charlie Barnett from outside the box goes harmlessly over the bar.
44:44 Free kick crossed right-footed by Charlie Barnett from right channel, clearance made by Tamika Mkandawire.
44:44 Booking Charlie Daniels shown a yellow card.
44:34 Free kick awarded for an unfair challenge on Aaron Cresswell by Charlie Daniels.
42:00 Free kick taken by Luke Summerfield.
42:00 Booking Craig Curran goes into the referee's book for unsporting behaviour.
41:47 Free kick awarded for a foul by Craig Curran on Andros Townsend.
39:16 Marlon Broomes gives away a free kick for an unfair challenge on Scott McGleish. The free kick is delivered left-footed by Andros Townsend from left channel, Ash Taylor manages to make a clearance. Corner taken right-footed by Luke Summerfield from the right by-line to the near post, Close range header by Tamika Mkandawire goes over the bar.
38:34 Charlie Daniels concedes a free kick for a foul on Craig Curran. Chris Shuker restarts play with the free kick.
36:58 Effort on goal by John Welsh from long range goes harmlessly over the target.
36:24 Aaron Cresswell is adjudged to have handled the ball. Glenn Morris takes the free kick.
34:59 Ian Thomas-Moore crosses the ball.
31:36 Free kick awarded for a foul by Jimmy Smith on Zoumana Bakayogo. Chris Shuker crosses the ball in from the free kick, clearance made by Ben Chorley. Inswinging corner taken by Chris Shuker from the left by-line, Scott McGleish manages to make a clearance.
31:25 The offside flag is raised against Ryan Jarvis. Aaron Cresswell restarts play with the free kick.
30:53 Craig Curran is ruled offside. Direct free kick taken by Glenn Morris.
29:49 Inswinging corner taken by Sean Thornton from the left by-line played to the near post, clearance by Ash Taylor.
29:00 Assist on the goal came from Paul McLaren.
29:00 GOAL - Charlie Barnett:Leyton Orient 1 - 1 Tranmere Charlie Barnett scores a goal from close range high into the middle of the goal. Leyton Orient 1-1 Tranmere.
28:52 Centre by Craig Curran, clearance made by Ben Chorley.
27:22 Substitution Aaron Cresswell replaces Ian Goodison.
25:20 Free kick awarded for an unfair challenge on Ryan Jarvis by Marlon Broomes. Luke Summerfield fires a strike on goal direct from the free kick, Scott McGleish gets a block in. Outswinging corner taken from the right by-line by Luke Summerfield.
24:33 Handball decision goes against Sean Thornton. A cross is delivered by Chris Shuker, Ian Goodison takes a shot. Save by Glenn Morris.
23:04 Assist by Ryan Jarvis.
23:04 GOAL - Scott McGleish:Leyton Orient 1 - 0 Tranmere A goal is scored by Scott McGleish from the edge of the penalty box to the bottom left corner of the goal. Leyton Orient 1-0 Tranmere.
22:01 Chris Shuker has an effort from just inside the box that misses to the left of the target.
20:25 Free kick awarded for an unfair challenge on Charlie Daniels by Paul McLaren. The ball is swung over by Andros Townsend, Scott McGleish has a headed effort at goal from just inside the area that misses to the right of the goal.
20:01 Centre by Craig Curran, Tamika Mkandawire manages to make a clearance.
18:53 Shot by Zoumana Bakayogo from deep inside the penalty area misses to the right of the goal.
18:13 The ball is delivered by Charlie Barnett, clearance by Charlie Daniels.
17:50 A cross is delivered by Craig Curran, clearance by Ben Chorley.
16:58 Sean Thornton fouled by Paul McLaren, the ref awards a free kick. Glenn Morris takes the free kick.
16:14 Zoumana Bakayogo sends in a cross, save made by Glenn Morris.
15:31 Effort on goal by Scott McGleish from deep inside the penalty area misses to the right of the goal.
14:54 Andros Townsend delivers the ball, save by Luke Daniels.
14:05 Luke Summerfield has an effort at goal from a long way out that goes wide left.
13:57 The ball is crossed by Stephen Purches, clearance made by Marlon Broomes.
13:20 The ball is crossed by Charlie Barnett, Stephen Purches makes a clearance.
11:12 Craig Curran takes a shot. Save by Glenn Morris.
10:28 A cross is delivered by Andros Townsend, Ryan Jarvis produces a right-footed shot from the edge of the box and misses to the right of the goal.
8:00 Centre by Sean Thornton, blocked by Marlon Broomes. Inswinging corner taken from the left by-line by Sean Thornton, clearance made by Marlon Broomes.
5:54 Free kick awarded for an unfair challenge on Ryan Jarvis by Ash Taylor. Sean Thornton produces a shot on goal direct from the free kick, blocked by Ian Goodison.
3:16 Free kick awarded for a foul by Jimmy Smith on Ian Thomas-Moore. Direct free kick taken by Chris Shuker.
2:55 The ball is sent over by Zoumana Bakayogo, clearance by Tamika Mkandawire.
2:34 Chris Shuker delivers the ball, Tamika Mkandawire manages to make a clearance.
2:06 Unfair challenge on Zoumana Bakayogo by Jimmy Smith results in a free kick. Ian Goodison restarts play with the free kick.
0:25 Free kick awarded for a foul by Chris Shuker on Sean Thornton. Sean Thornton restarts play with the free kick.
0:00 The referee starts the match.
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