FA Cup semi-finalists Cardiff also suffered the blow of having striker Jimmy Floyd Hasselbaink sent off for violent conduct, leaving the ex-Leeds and Chelsea striker facing up to a three-match suspension.
But the Welsh club are set to appeal against the decision.
The visitors were on the back foot for most of the afternoon, but they grabbed the lead with a shot out of the blue after just 11 minutes with what was their first attack of the game.
Paul Parry pounced on to a quickly taken throw-in and he beat keeper Dean Gerken with a shot from outside the box which soared into the top corner of the net.
After that, it was mostly a case of defending for Cardiff and they were fortunate when referee Kevin Wright waved away strong Colchester appeals for a penalty for a clear tug on Kevin Lisbie.
And Lisbie was cursing his luck again when he struck the far post with a close-range shot on the half-hour mark.
Cardiff were reduced to ten men in the 62nd minute when Hasselbaink was dismissed for violent conduct.
It seemed a harsh decision, as both he and Gerken contested a loose ball. Hasselbaink's boot was high and it struck Gerken in the face, but there seemed to be no malice in the challenge.
However, the Cardiff striker was sent off and his side conceded an equaliser after 71 minutes thanks to a fantastic strike from Johnnie Jackson.
The goal stemmed from a corner with Medy Elito's cross dropping into the path of Jackson, who let fly with a rasping 25-yard half-volley that crashed into the roof of the net.
It was former Tottenham midfielder Jackson's seventh goal of the season and it gave the U's genuine hopes of stealing a winner late on.
However, Cardiff clung on despite the home side earning five corners in injury time.
This result stopped a run of five straight defeats for bottom club Colchester, although they still look doomed to play League One football next season.
External Reports
ColchesterUtd.com
The Telegraph
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Wales On Sunday