David Wright marked his return to action after injury with a 90th minute equaliser to earn the reserves a derby draw.
The Town defender was making his first appearance since sustaining an ankle ligament problem in the opening day defeat by Preston and rose highest to head in from a corner to round off Blues' second comeback of the game.
Colchester were two goals up in the first 20 minutes, Mitch Nelson heading in a free-kick then Akanni-Sunday Wasiu extending the lead with a close range finish.
Jordan Rhodes pulled one back for Town before the break but Colchester made it 3-1 on 58 minutes through Fabian Batchelor.
Ivan Campo played the first hour as he added to his match fitness, with David Norris staying on for the full game as he continues his recovery from heel surgery.
Dean Bowditch reduced the arrears on 75 minutes and Wright preserved Town's lengthy unbeaten run in League reserve team football with that last minute header.
