Steven Gillespie's penalty was enough to earn Colchester a narrow victory.
Gillespie had earlier been denied by Orient keeper Glenn Morris' one-handed save and then hit a shot across goal.
But he made no mistake from the spot just before the break after O's defender Tamika Mkandawire was adjudged to have handled a Dean Hammond cross.
O's Adam Boyd then had a penalty saved by Jimmy Walker before Sean Thornton was dismissed for a second yellow and Colchester's Dave Perkins hit the bar.
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