A late Stephen Dawson strike won the match for Orient and booked them a third round date at Blackburn following a 3-2 success against Bristol Rovers.
Orient opened the scoring when David Mooney delicately poked the ball beyond Scott Bevan 18 minutes in.
Just five minutes later, Ben Chorley doubled the hosts’ advantage when he converted from the penalty spot as Orient looked comfortable.
Chris Zebroski hit back for the visitors with 20 minutes to play to set up a nervy finish and substitute Elliot Richards struck in injury time to level the match.
The O’s weren’t done though and captain Dawson won the match in the final minute of injury time.
Russell Slade made one change for following Saturday’s defeat to Carlisle as Terrell Forbes got his first start of the season.
Forbes came in for Elliot Omozusi who dropped to the bench, while Moses Odubajo was also included among the substitutes.
David Button continued in goal for the O’s while Mooney and Jamie Cureton started up front together.
Rovers included former Orient striker Scott McGleish in their starting line up as the veteran went in search of a goal against his former employers.
The visitors saw off higher division opposition in round one and were pressing early on as they sought a repeat showing.
Mustapha Carayol enjoyed the first chance of the match five minutes in but it was a tame effort inside the box and went well wide of Button’s left hand post.
The O’s were starting to string together some good passes and did manage to stick the ball in the net but the whistle had already blown.
Mooney was unable to keep the ball in play before crossing for Dean Cox to tap in but the goal was correctly disallowed.
The home side’s movement paid off shortly after when they took advantage of a wayward pass to grab the lead.
Craig Stanley looked to centre the ball but found only Cox as opposed to a team mate and the Orient wide man was able to lift a beautiful ball over the defence for Mooney to prod beyond the onrushing keeper.
Five minutes later, the O’s were to double their lead following a swift counter attacking move.
Jimmy Smith reacted quickest to break away from the back and with Rovers stretched, his pass found Cox.
The tackle came in to deny the winger but with Mooney picking up the loose ball, the Irishman tumbled under the challenge of Wayne Brown giving the referee no choice but to award the penalty.
Chorley stepped up to the plate and made no mistake, passing the ball firmly into the bottom left corner.
The O’s were playing with confidence at this point, passing the ball with ease all over the pitch and still looking to add another goal.
Cureton had a chance on the half hour when Cox crossed low for him on the left but the forward’s shot on the turn was comfortably high and wide.
Button was called into action as the half drew to a close, saving well to his right to deny a long range effort from Stanley but the half belonged to the O’s.
A late attack saw Charlie Daniels charge down the left to win a corner which Smith managed to get his head to but the chance fell just the wrong side of the post.
Deep into injury time, Cox’s short free kick to Chorley resulted in the defender letting fly with a fierce low drive from distance, only missing by inches as the hosts took a two goal lead at half time.
The O’s made the quicker start after the break and could have had a third a couple of minutes in.
Leon McSweeney’s cross from the right was nodded back by Cureton to an unmarked Mooney but the former Reading forward was unable to control the bouncing ball, sending his effort over the bar.
Daniels tested Bevan with a free kick on 55 minutes but the visitors went straight up the other end to give Orient a scare.
Lee Brown found himself in an advanced position and turned the O’s defence inside out before his curling effort, destined for the net, was brilliantly tipped on to the post by Button.
The game petered out somewhat with few chances being created but the earlier miss was a warning sign as Rovers reduced the deficit after 69 minutes.
Zebroski cut into the middle from a wide position, inadvertently exchanging passes with Wayne Brown before slamming home in the middle of the box.
Slade’s side didn’t let it affect them though and went in search of the move that would restore their two goal lead immediately, with Cureton lobbing Bevan, only to be denied by the crossbar.
With few chances created in the wake of Cureton’s miss, the O’s received a further scare when Button looked to be in a lot of pain following a brave dive at McGleish’s feet.
The stopper was able to continue though but he was to concede a matter of minutes later.
A cross from the right was nodded down for Richards to fire low beyond Button but the O’s were not to be denied.
A surging run from Téhoué ultimately fell to Dawson who kept his cool to fire home in the last minute.
Orient: Button; Cuthbert (Laird 38), Chorley, Forbes, Daniels; Smith, McSweeney (Omozusi 65), Dawson, Cox; Mooney (Téhoué 82), Cureton.
Subs: Butcher, Porter, Odubajo, Richardson.
Rovers: Bevan; Smith, Virgo (Woodards 34), Anthony, L Brown; W Brown, Stanley, Gill (Campbell 71), Carayol (Richards 76); McGleish, Zebroski.
Subs: Cronin, McLaggon, Jeffries, Hunter.
Attendance: 1,881 (397)
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