Peterborough, who won the Football League Trophy at the English national stadium on Sunday, moved four points clear of seventh-placed Swindon Town and Darren Ferguson's men still have a game in hand.
It was a workmanlike display from the hosts, who scored in either half through Tommy Rowe and Britt Assombalonga to put back-to-back league defeats behind them.
A third defeat in a row leaves Colchester just three points above the relegation zone in a congested bottom seven.
Rowe opened the scoring with a well-placed header from Grant McCann's 26th-minute corner and the visitors struggled to mount any meaningful response.
Colchester were the architects of their own downfall for the second, which effectively ended the match as a contest, with a defensive error handing Assombalonga his 29th goal of the campaign.
