The visitors snatched a point when Gavin Johnson fired home from 25 yards after a short free-kick to deny Barnsley in their final home game of the season.
Tykes caretaker boss Andy Ritchie was furious with the referee for awarding the free kick in the first place, and although the visitors duly benefited, a draw was perhaps a fair result.
The home side had earlier taken the lead when Daniel Nardiello headed home at the far post after great work by Nicky Wroe four minutes before the break.
The goal was perhaps on the cards as Barnsley had already wasted three good chances.
Michael Chopra went close with the game only two minutes old when his right-foot shot was well saved by Colchester keeper Aidan Davison.
Simon Johnson blazed over when well placed and then clipped the bar with a similar effort before Nardiello eventually broke the deadlock.
Colchester did not threaten much in that 45 minutes, although Johnson did come close to finding the net when he headed wide earlier on.
The visitors were much better in the second half and almost drew level when Neil Danns headed into the side netting from close range.
Barnsley goalkeeper Scott Flinders then made a brilliant point-blank save to deny Marino Keith with only six minutes to go.
At the other end Barnsley had chances to put the result beyond doubt as Chopra wasted a good opportunity when he was denied by a late tackle after taking to long to shoot.
Stephen McPhail also came close but his effort from the edge of the area just flashed the wrong side of the post.