The U's surrendered their one-goal advantage in second half stoppage time as Leyton Orient come from behind to take a point.
A tense first half preceded a much more open second period, with both sides scoring two goals and holding the advantage at some point.
The U's fell behind to a spectacular Ruel Sotiriou strike before fighting back to take the lead with two goals in three minutes from Myles Kenlock and Owura Edwards.
But Wayne Brown's side conceded a ninety-third minute equaliser as Ethan Coleman bundled the ball home in a crowded penalty area.
Wayne Brown made two changes to the side that drew 1-1 against Oldham Athletic on Saturday afternoon, with Tommy Smith and John Akinde on th bench, replaced by Freddie Sears and Myles Kenlock.
Also on the bench was Corie Andrews, who took Brendan Wiredu's place in the matchday eighteen for Colchester United.
A slippery surface made if difficult for intricate play throughout the first period of the game, with rain still coming down at the JobServe Community Stadium, and as such, there were few chances in the opening half hour of the game. With both sides reduced to playing long balls forward, there were just a couple of half chances falling to Freddie Sears and Alan Judge.
Sears saw his deflected effort fly just over the top of the cross bar, while Alan Judge's free kick didn't quite dip in time to trouble the Chilean 'keeper.
At the other end of the pitch, Shamal George would have been nervous to hear the referee's whistle blow after Sotiriou had gone down near him. But the official saw it as simulation from the Cypriot and booked the Orient forward in the eleventh minute of the game.
Wayne Brown was forced in to his first change of the game eariler than he would have liked after Cole Skuse picked up a knock, having to be replaced by Emyr Huws with just under thirty minutes played.
But neither side was able to break the deadlock through an intruiging first forty-five minutes.
The U's thought they had found the breakthrough eight minutes into the second period when Owura Edwards tapped the ball beyond Vigouroux into the back of the net. The on-loan winger had connected with Noah Chilvers' driven cross, only for the flag to be reaised and offside to be given against the U's man.
It took something special for the deadlock to be broken, and the visitors did just that with Ruel Sotiriou smashing home an unstoppable effort from outside the area. Coleman collected the ball from George's mis-hit clearance, playing it to Sotiriou who blasted his effort in off the underside of the crossbar to give his side the lead.
The O's lead wouldn't last long though, as Myles Kenlock levelled the game with his second U's goal on seventy-five minutes. Noah Chilvers battled to win a corner for his side, and Alan Judge delivered to the back post, with Kenlock obliging with a simple header at the back post to make it 1-1 with fifteen minutes to play.
And it wasn't level for long, as Wayne Brown's side got their noses in front for the first time in the game four minutes later. John Akinde nodded the ball back across the face of goal with Owura Edwards arriving late at the back post to smash beyond Vigouroux and send the home crowd wild.
But there was another twist in the tail of an entertaining second half at the JobServe Community Stadium as Ethan Coleman capitalised on a scramble in the goalmouth to poke the ball home in stoppage time and earn his side a point.
The point means the U's move up one place to twentieth in the table, overtaking Stevenage on goal difference, now sitting on thirty-three points from thirty-four games.
Up next for Wayne Brown's side is the final home game of the quartet, with Port Vale making the trip to Essex on Saturday afternoon.
Colchester United starting XI: George, Chambers, Hannant (Akinde 68'), Skuse (Huws 23'), Judge, Sears, Edwards (Tchamadeu 87'), Chilvers, Dallison, Kenlock, Coxe.
Unused subs: Hornby, Smith, Andrews, Tchamadeu, Wright.
Leyton Orient starting XI: Vigouroux, Wood, Thompson (Tanga 89'), Smith, Pratley, Beckles, Sotiriou, Young (Smyth 67'), Khan (Kyprianou 56'), Coleman, Ray.
Unused subs: Moss, Ogie, Byrne, Obiero.