Goals from second-year scholar Kyran Wiltshire and Daniel Powell saw Karl Robinson's side come from behind after David Cassidy's strike had put the Irish Premier Division team in front.
Cassidy scored after 27 minutes following a lovely turn and delicate lob over goalkeeper David Martin.
Robinson's men were level on the hour-mark as Wiltshire fired home the rebound after Jay McEveley, on trial with the Dons after leaving Swindon, had seen his shot saved.
Recent signing Tom Hitchcock had the ball in the net in the 88th minute, but his effort was ruled out for offside.
But the Dons won the game a minute later when the impressive Powell raced on to a throughball, rounded the goalkeeper and coolly slotted the ball home.