But Portuguese star Cristiano Ronaldo continued his rich vein of scoring form when he hit the equaliser after Ruud van Nistelrooy was sent on, a substitution that proved a master stroke.
And deep into injury-time, Louis Saha's shot came back off the post and struck Chimbonda and went in to complete a United smash and grab they hardly deserved.
Wigan were intent on revenge after their Carling Cup final disappointment eight days ago and manager Paul Jewell was out of avoid yet another defeat at United's hands, having lost his four previous clashes against Sir Alex Ferguson's team, all by a 4-0 margin.
It was another full house at the JJB Stadium and further cosmetic surgery had been carried out to improve the playing surface, relaid just before Christmas at a cost of around £100,000.
The Latics had John Filan making his first Premiership start since November, taking over from luckless keeper Mike Pollitt, who is facing a six-week lay off with hamstring trouble.
Scottish star Lee McCulloch was restored to the starting line-up and Scharner was preferred to Stephane Henchoz at the back.
United stuck with the Cardiff line-up, meaning leading scorer van Nistelrooy again had to be content with a place on the bench.
The first half provided plenty of high tempo action but no goals, although determined looking Wigan had more chances to break the deadlock.
Gary Teale, who picked up his first Scotland cap last week, produced the first threat after being played in by Henri Camara. But the ball bobbled badly as he struck it and flew way over the target.
Camara flashed the ball across the face of the United goal with no one there to get the vital touch, and the Senegal striker was just inches away with a left-foot snap-shot after a flick-on from McCulloch.
Edwin Van de Sar kept out a Jason Roberts header, McCulloch hit another shot wide, Graham Kavanagh was out of luck when he twice failed to hit the target with first-time efforts, and in stoppage time, Roberts again went tantalisingly close.
United were restricted to just a couple of chances in the opening 45 minutes.
Ronaldo whistled a free-kick just over the bar and England star Wayne Rooney wasted a great opportunity when he looked to play in Saha instead of shooting.
United should have taken the lead early in the second half when Gary Neville banged in a terrific cross from the right, but the killer touch again deserted Rooney who put his header over the bar from 10 yards.
Then Wigan got the reward they deserved by snatching a goal from a Jimmy Bullard corner.
Arjan de Zeeuw's header was cleared off the line by Ryan Giggs and Van de Sar blocked the follow-up from Roberts, but it fell to Scharner and the Austrian defender finished it off.
A minute later United were rocking again and needed their goalkeeper to get down low to keep out a powerful shot from Roberts.
United sent on van Nistelrooy for Ji-Sung Park and it paid off almost instantly when the Dutchman supplied the cross for Ronaldo (who was arrested on rape allogations over the summer) to sweep in the equaliser.
Skipper de Zeeuw almost restored Wigan's advantage with a header as both sides went in search of a winner, before United had a penalty appeal turned away when Rooney went down under a challenge from Chimbonda.
It looked like both would have to settle for a point - until that cruel finish.