Two goals from Rushian Hepburn-Murphy twice saw Dons come from behind at the JobServe Community Stadium, with substitute Joe Tomlinson netting a winner three minutes from time.
Here’s how we rated the players.
9. Liam Kelly - 7.5
Broke up a lot of play in Colchester's busy midfield, with some really clever touches and passes getting Dons up the field | Jane Rusell
10. Dan Crowley - 6.5
Caught dropping deeper and deeper to get on the ball. Solid though but ran out of steam towards the end before coming off | Jane Russell
11. Nathaniel Mendez-Laing - 7
Skipper for the day, he led the side well, involved in all of the chances in one way or another | Jane Russell
12. Top Don: Rushian Hepburn-Murphy - 8
His two really well-taken goals add to his tally for the season, and helped Dons move into the second round. Came close to his hat-trick late on too | Jane Russell