There was an unmistakable end-of-season to this game, with neither side having anything urgent to play for.
Orient assured their survival last week, while the U's promotion dreams died long ago, but there was no sign of any gulf in class between the two sides.
The game was settled in favour of the U's in the final minutes.
Kevin Lisbie hammered home from the penalty spot in added time after Luke Ashworth was sent off for saving Clive Platt's goal-bound shot on the line.
It was not an ideal way for boss Russell Slade and the players to complete a campaign in which they have been revived since the new manager arrived.
Now Orient end the campaign in 18th position in League One, and that is just fine for the massed ranks of Orient fans who sang from kick-off to final whistle, today.
It was them who provided the best entertainment in this low-tempo contest, with anti-Southend chants and others aimed at the home fans.
In the second half a line of them did a conga along the foot of stand in the absence of anything very interesting to look at on the pitch.
Orient had only to avoid an embarrassing capitulation at the gleaming Weston Homes Community Stadium today, but they looked good value for a win here.
Slade was forced to field patchwork back-line, because of injuries to Charlie Daniels, Tamika Mkandawire and Stephen Purches.
But Ashworth and Andrew Cave-Brown stepped up well and they kept striker Kayode Odejayi subdued, and the attack threat from Anthony Worsworth and Ashley Vincent, as well.
The momentum swung between each team throughout the game, and Orient matched the U's with Slade's brand of push-and-play.
Chances were at a premium for each side. Sean Thornton had the first shot of the game on 20 minutes which was blocked.
The Irishman headed over from John Spicer's corner on 27 minutes, which was won by the visitors after a great combination of passes between McGleish, Jarvis and Lichaj which unpicked the U's back-line inside the box.
Thornton was the catalyst for Orient in midfield as he been so often.
In the second half things continued as they had done before. Ryan Jarvis caused a stir with a snap-shot from a long ball on the hour-mark which keeper Ben Williams tipped over the bar.
Three minutes after that, John Spicer fired low into Williams' arms from Chambers' neat lay-off, as Oient supplied some excitement.
Slade must have sensed that out-of-form Colchester were for the taking when he put on Jason Demetriou for Jimmy Smith, on 70 minutes.
His first contribution was so release Jarvis down the left flank with a neat dinked pass. Jarvis steamed on and his low cross across the face of goal caused chaos. Chambers blazed a shot which Marc Tierney blocked by throwing himself at it.
Colcester snatched the victory which their play did not really deserve in added time. Lisbie made no mistake from the spot.
But the main thing is that Orient have successfully solved the relegation crisis which threatened to sink the club, not so long ago.
Jones, Chorley, Ashworth, Chambers, McGleish (Scowcroft), Thornton, Jarvis, Cave-Brown, Spicer, Smith (Demetriou 70), Lichaj.
Subs: Giddens, Pires, Baker, Cestor Mike, Patulea.
Attendance: 5,751 including 1,197 Orient fans.
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