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The U's, already assured of finishing in their highest position since they won promotion to Division 2 in 1998, netted twice just before the interval but Wigan dominated the second half and substitute Neil Roberts bagged a brace to earn the Lancashire visitors a deserved draw.
A rather low-key first half burst into life in the 42nd minute when striker Scott McGleish, spotting keeper John Filan off his goal, fired home in spectacular fashion from 35 yards.
United were really in the driving seat when Charlie MacDonald plundered a second goal in first-half injury time. MacDonald's first effort was blocked by keeper Filan. but he crashed the loose ball into the roof of ther net.
It was MacDonald's first goal for the club since his loan move from Charlton.
The striker is set to be released by the Londoners on a free transfer this summer, so he could be back at Layer Road next season.
Wigan pulled a goal back on the hour mark when substitute Roberts, who'd only been on the pitch for 10 minutes, slotted home following a fine through ball from Andy Liddell.
And the visitors were back on level terms in the 86th minute. Roberts sneaked in at the far post to head home Liddell's cross, although Colchester players were convinced that the cross had actually swerved out of play before landing on the head of the delighted Roberts.
Colchester have now ended the season with the same number of points - 57 - as 12 months ago.
Their manager Steve Whitton said : "Just surviving in this Division is success for a club like us.
"Wigan have spent so much money on players so it's remarkable that we are even able to compete with them."
Before the kick-off Karl Duguid enjoyed a clean sweep of all the senior 'player of the year awards' for Colchester.
Duguid said :"It's a very proud day for me. It was great to receive the awards from the supporters, especially as I didn't play that well last season and got a bit of stick from them.
"It was also great to be named the player of the year by my teammates. They are the professionals who I play with all season," added Duguid, who made an appearance as a second half substitute following a recent knee injury.