Orient have been comeback kings of late, but Russell Slade's side today showed they can hold onto a lead as well.
Jason Brown in goal turned in a man-of-the-match with a string of saves to keep Orient ahead.
Goals by Stephen Dawson on 10 minutes and then Scott McGleish in first half injury time put the visitors ahead.
But after that it was all one-way traffic as stung Rovers went on the attack at Prenton Park.
Sam Wootton's header dragged them back into it on 62 minutes.
Brown then was a one-man wall against a barrage by the hosts in a nerve jangling match.
The on-loan keeper from Blackburn Rovers denied Enoch Shownumi and Lateef Elford-Alliyu among others during a mad 15 minute spell.
When Brown was beaten the cross-bar rescued Orient from Ian Goodison's volley with just six minutes left.
Near the final whistle, John Welsh saw his effort just graze Brown's post.
Orient will be well pleased with this win, sealed by good play at each end of the pitch.
It was backs to the wall defending for them after McGleish and Dawson's goals.
The Irishman struck when Rovers failed to clear Charlie Daniels free-kick into the mixer from a foul on Matt Spring, on 10 minutes.
After that, Orient's patched-up defence was often under massive strain by Rovers.
But then Scott McGleish doubled Orient's advantage when he struck right before the half-time whistle, tapping home after keeper Gunnar Nielsen spilt Paul Jose M'Poku's shot.
It was all Tranmere after break and Rovers finally got the goal they needed.
Scott Wootton headed home when he rose to meet Aaron Cresswell's free kick, on 62 minutes.
Aaron Brown conceded the foul halfway up midfield for a challenge on Thomas-Moore which drew a yellow card.
Five minutes later Revell went so close with a header just wide at close range, from Jimmy Smith's cross.
In end-to-end scenes, Omozusi then slid in to block substitute Lateef Elford-Alliyu's shot from ten yards.
Keeper Brown was superb to deny him on 69 minutes with a low one-handed save to his near post.
It was all one-way traffic for a long time with Orient under the cosh. The yellow card for Aaron Brown made things more complicated for the O's.
Tranmere kept on the attack. Keeper Brown was classy again with a fine double save to keep first Showunmi and then Jennings on 75 minutes.
He was at it again on 79 minutes with another sharp save inside a crowded penalty area.
Ian Goodison slammed a volley against the bar on 84 minutes.
Orient dug deep and showed great character today in the face of all out attack for three very well-earned points.
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