Despite a strong opening 45 minutes, Dons went in level after Anthony Scully’s penalty cancelled out Stephen Wearne’s opener - the first goal on the road this season for Mike Williamson’s side.
A Fiacre Kelleher strike nine minutes after half-time then secured the points for Colchester.
Here’s how we rated the players
1. Nathan Harness - 5
Had next to nothing to do for the most part. Was beaten by a penalty before he flapped at a corner which led to the second goal for Colchester | Jane Russell
2. Dean Lewington - 6
A solid outing, but was adjudged to have given away a penalty which looked extremely soft | Jane Russell
3. Luke Offord - 6.5
Kept his place in the side after Saturday. Defended pretty well, keeping the Colchester front line quiet | Jane Russell
4. Jack Tucker - 6.5
Provided a great assist for Wearne's goal, and got to show off some of his long-range passing too | Jane Russell