Magnus Okuonghae spooned a shot over from eight yards early on for Colchester.
But the Dons took a 12th-minute lead when Daniel Powell finished coolly low past U's keeper Sam Walker after a swift break by the visitors.
Walker pushed away Powell's first-time shot soon after but Colchester warmed to the task, with Gavin Massey's deflected low shot sailing into the side-netting for a corner.
Freddie Sears' hooked shot on the turn came back off the post and Billy Clifford and Andrew Bond both went close before half-time as the U's finished the first half strongly.
But Walker parried away Patrick Bamford's strike early in the second half and the Dons wrapped up their win with 12 minutes to go through Bamford, who planted a low shot past Walker after Luke Chadwick's pass has split the defence.