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.
‘He instantly popped into our ratings as one of the best U21 midfielders in Europe. The impressive thing is Slot has made him into more of a no.6' Inside Ryan Gravenberch's transformation at Liverpool
‘I don’t think Liverpool would look at Ollie Watkins, a striker isn’t a pressing issue for them – it’s Arsenal who need one’ Former Reds star explains why his old club don’t need an out-and-out forward this summer
