Orient’s play-off push all but ended as two goals in the opening 24 minutes from Gavin Massey and Drey Wright earned Colchester a narrow win.
O’s top scorer Kevin Lisbie cut the deficit just before the break and then missed a second-half penalty as Orient piled on the pressure in a desperate bid to keep their season alive, but it was Colchester that held on to ease their relegation fears.
Orient still have a mathematical chance of a top six finish, but realistically they are destined to be playing League 1 football again next season.
It was a makeshift Orient side that manager Russell Slade sent out for this vital clash. With just one recognised centre-half available.
Without injured defensive trio Scott Cuthbert, Mat Baudry and Elliot Omozusi, Slade paired central midfielder Romain Vincelot with skipper Nathan Clarke at the heart of the visiting defence and could he could name just five players for a threadbare, raw-looking bench.
Both sides needed maximum points for very different reasons, but it was the home side who looked to have taken a giant stride towards League 1 safety with two goals in the opening stages
O’s struggled to contain the aerial threat of Colchester duo Jabo Ibehre and Clinton Morrison, but it was not only at the back where the visitors struggled as they failed to retain the ball.
The home side were forced into a reshuffled after 12 minutes when defender Josh Thompson limped off with a hamstring injury and was replaced by Bradley Garmston and it was the Colchester substitute who had a hand in the opening goal.
It arrived on 20 minutes when former O’s striker Ibehre was allowed time and space to control the ball before sweeping it out to Garmston who was galloping down the left and his cross was met by Massey, who sent a header exploding into the net from six yards out.
Four minutes later Orient’s slim play-off chances looked dead and buried when the home side struck again. This time Morrison used his strength to hold off a challenge and fed Wright who turned and fired home from eight yards with an effort that took a deflection off Vincelot.
But Colchester’s fragile confidence started to drain away as Orient retained the ball better and the home defence looked anything but safe.
And when they were caught square on 37 minutes Lisbie raced onto a hopeful through ball from Dean Cox and despite Colchester’s claims for offside the veteran striker showed great composure as he slotted the ball past Sam Walker for his 15th goal of the season.
Two minutes later Leon McSweeney arrived on the end of a move and fired just wide as Colchester started to rock.
With both sides looking unsure at the back Orient’s best hope of success was to continue pushing forward and they started the second half on the front foot as Shaun Batt replaced the former Colchester man Lloyd James in a tactical switch.
Jimmy Smith moved to the centre of midfield and Batt played down the right as O’s continued to press.
But it was Colchester who almost added to their advantage on 58 minutes when Ibehre broke clear down the right, but dragged his shot just wide of the far post.
O’s continued to dominate and had a great chance to level from the spot on 77 minutes when Batt powered down the right and was tripped in the box by substitute Garmston.
Lisbie stepped up, but keeper Walker dived to his right and parried the striker’s spot-kick and the home side smuggled the ball away for a corner.
The O’s striker almost made amends three minutes from time with a header following a Dean Cox corner on the left, but again Walker saved well, this time clawing the effort away from under his bar – and with it went Orient’s hopes of a point and their play-off dream.
Colchester United: Walker; Wright, Okuonghae Thompson (Garmston 12), Wilson; Massey, Clifford (O’Toole 65 mins), White, Wright; Morrison (Smith 76 mins) Ibehre.
Subs: Cousins, Bond, Bean, Compton.
Colchester goals: Massey (20 mins), Wright (24 mins)
Colchester bookings: Garmston (35 mins unsporting behaviour), Wilson (83 mins foul)
Leyton Orient: Jones; Odubajo, Clarke, Vincelot, McSweeney; Smith, Rowlands, James (Batt 45 mins), Cox; Lisbie, MacDonald (Obafemi 84 mins). Subs: Sawyer, Lee, Vanderhyde.
Orient goals: Lisbie (37 mins)
Orient bookings: None
Attendance: 4.704 (inc 1,158 Orient fans)
Referee: R Clark (Northumberland).