A thrilling final 11 minutes to Saturday's game at Brisbane Road saw Orient concede an equaliser before Moses Odubajo and Shaun Batt combined superbly on the counter-attack to snatch a third win in as many games for the home side.
David Mooney had fired the O’s in front with 21 minutes gone, expertly controlling an in-swinging Dean Cox cross from the left and thumping his volley into the roof of the net from eight yards out, sending Orient into the break with a deserved 1-0 lead.
A much improved second-half performance from the visitors was rewarded with an equaliser in the 79th minute when substitute Marcus Bean beat a crowd of players to the ball to head past Eldin Jakupovic, who had another storming game between the posts for Orient.
Colchester looked to be in the ascendancy after pulling level but brilliant link-up play on the break between Odubajo and Batt sent the former through on goal, and he kept his composure well to bag his 10th goal of the season and a crucial three points for his side.
Both Orient and the U's made two changes from the teams they sent out in their last fixture.
O’s defender Mathieu Baudry was suffering from a slight hamstring injury which meant Scott Cuthbert was moved back in to the centre of defence with Gary Sawyer filling in at left back, while Kevin Lisbie returned to the home side's starting XI in place of Chris Dagnall.
Lisbie’s re-introduction to the team meant that the O’s lined up with four players who have had spells with Colchester in the past – David Mooney, Lloyd James and skipper Nathan Clarke being the others.
After losing in the final minutes to Sheffield United in midweek, visiting boss Joe Dunne replaced Bean and experienced striker Clinton Morrison with Gavin Massey and Craig Eastmond, as they hoped to avoid losing a third game on the bounce.
By contrast, Orient's win on Saturday makes it a hat-trick of victories in a row, having beaten both Stevenage and Swindon 2-0 at Brisbane Road in the last two games of February.
It was an energetic start to the game from both teams with Freddie Sears looking particularly dangerous for the visitors, forcing Jakupovic into two early saves, though neither caused the Hull loanee too many problems.
Orient took longer to create any clear-cut chances but Odubajo was tormenting left-back Ryan Dickson with his mazy runs, while the winger's deliveries were also causing the rest of the visiting back four plenty of problems.
In fact, Odubajo won a corner courtesy of a tackle by Dickson on the byline which acted as a catalyst to the O's taking the lead on 21 minutes.
The initial delivery was cleared away by Colchester but, when Dean Cox sent a cross back into the box, Mooney got the better of his marker before unleashing an unstoppable volley high into the net past visiting keeper Sam Walker.
After scoring both of the O’s goals last week, Lloyd James was having another good game from the middle of the park, and it was his precise pass that allowed Lisbie the chance to double the home side’s lead not long after Mooney’s opener.
The midfielder's through ball allowed Lisbie to run free of the Colchester defence and the striker hit a good low shot which looked to be creeping inside the near post but Walker got down well to turn the ball behind for a corner.
Colchester continued to threaten with shots from range for the remainder of the first half but none came close to testing Jakupovic any further and the O’s carried a deserved 1-0 lead into the break.
The O’s keeper may have had a relatively straightforward opening 45 minutes but it didn’t take the opposition long to force him into action in the second period.
The U’s came flying out of the traps and a chance fell to Gavin Massey inside the 18 yard box in the opening minute - the winger brought the ball down well and sent a volley towards the bottom right corner of the net only for Jakupovic to make a stunning one-handed save.
Colchester kept the ball in play and sent it back over to Massey at the far post but the O's stopper somehow denied him not once but twice more before it finally went behind for a corner.
After recovering from that early scare, Orient enjoyed a number of good attacks, with wingers Cox and Odubajo both forcing Walker into saves.
However as the half progressed, the home side looked tired and Colchester began winning the midfield battle. The introduction of Bean just after the hour mark helped the visitors gain further control and it was the substitute midfielder himself who equalised for the U's.
Despite getting a hand to Bean's header on 79 minutes, Jakupovic was unable to stop the ball from sneaking inside the left-hand post to put the visitors on level terms.
Orient were under the cosh after Colchester scored and it seemed as though the away side were the most likely to get a winner.
However, after a long throw was launched into the Orient box on 83 minutes, the home side managed to work the ball away from danger and spark a lightning counter-attack.
Odubajo picked the ball up on the half way line before setting Batt free - the striker's first touch didn't look the best but he somehow managed to return a pass through two retreating defenders to Odubajo, who had continued surging forwards.
The winger raced through on goal before showing the composure of an experienced striker to slot the ball into the bottom left corner of the net and lift the roof inside Brisbane Road.
Orient might have extended their lead further as the game entered the final stages but were denied a strong penalty appeal and Cox fired over from close range after substitute Chris Dagnall's pull-back.
And the O's managed to defend their 18-yard box resolutely in the dying seconds of stoppage time as Colchester threw everything at them - ensuring they secured a valuable three points, emulating the score in the reverse fixture against the U's back in August.
ORIENT: Jakupovic, Omozusi, Cuthbert, Clarke (C), Sawyer, Odubajo, Vincelot, James (Bartley, 74), Cox, Mooney (Batt, 68), Lisbie (Dagnall (88)
SUBS NOT USED: Larkins, Lasimant, Simpson, Ness
GOALS: Mooney (21), Odubajo (83)
COLCHESTER: Walker, Wilson (C), Okuonghae, Eastman, Dickson, Eastmond (Bean, 60), Wright (Sanderson, 84), Sears, Vose (Bonne, 68), Massey, Ibehre
SUBS NOT USED: Cousins, Morrison, Olufemi, Sesay, Bonne
GOALS: Bean (79)
BOOKINGS: Eastmond (36)
REFEREE: David Webb
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