Both goals came in the first half with Harry Maguire equalising just before the break after Freddie Sears had given Colchester the lead.
The home side made the early running with Tony McMahon's curling effort going wide and Sean McGinty shooting straight at keeper Sam Walker.
But it was Colchester who took a 25th-minute lead when they caught their opponents on the break following a corner. Sanchez Watt advanced towards the penalty area before slipping the ball to Sears who beat George Long with a low shot.
Maguire (45) equalised with the help of an error from keeper Walker after firing a shot on target. Walker appeared to have it covered but the ball squirmed from his grasp and went just inside his left-hand post.
Walker atoned for his earlier error with saves from Lyle Taylor and Conor Coady, and also reacted smartly to beat Taylor to Fabien Brandy's ball through the middle.