The visitors dominated the opening stages and had created several chances before Dele Adebola put a spectacular diving header into his own net on 30 minutes.
The striker has not scored at the correct end for the Sky Blues since September and looked unlikely to fare any better against Colchester despite Coventry's adventurous four-up-front formation.
The goal came after man-of-the-match Wayne Andrews had shot narrowly wide from the edge of the box and had another effort blocked.
However, the goal spurred City into life and they restored parity three minutes later with their first effort on target.
Andy Morrell played in Julian Joachim who turned well and headed straight for the box. He looked to have run out of room only for Richard McKinney's clearance to rebound off the striker and sail into the net.
City then seized the initiative and Gary McSheffrey looked lively, blazing narrowly over from 12 yards just before the break, and forcing a save from McKinney shortly after the interval.
McSheffrey should have done better on 50 minutes when he unselfishly opted to play in Morrell when a shot looked the better option, and his pass was too far in front of his team-mate.
Colchester then came inches from producing a shock when Andrews reached the by-line and pulled the ball back for Scott McGleish, whose close-range shot was tipped on to the post by Gavin Ward.
Coventry also hit the woodwork, with a sublime 25-yard effort from substitute Stephen Warnock beating McKinney but rattling the crossbar.
Debutant Bjarni Gudjonsson almost made an instant name for himself with ten minutes to go when the ball was put on a plate for him by City skipper Mo Konjic but his effort was well over.