Ultimately a disputed penalty awarded by referee Steve Bennett proved to be the only difference between the two sides.
However, there were also a couple of crucial saves from Chris Kirkland plus a vital clearance by Titus Bramble after a rare slip by the Wigan keeper.
The Latics were worth the three points though and Amr Zaki almost grabbed his second goal of the game in stoppage time when Joe Hart tipped his effort over the bar.
City brought back their big guns after the midweek Carling Cup shock against Brighton with Robinho back from his flying visit to Brazil and Joe Hart, Micah Richards and Shaun Wright-Phillips also among the returning stars.
Steve Bruce's problem was who to leave out after the win in the same competition at Ipswich on Wednesday. He opted to make one change with skipper Mario Melchiot returning to the starting line-up, and Paul Scharner dropping to the bench.
Egypt striker Zaki produced the first threat of the afternoon unleashing a fierce left-foot strike from the edge of the area after City had failed to clear a corner. Much to Hart's relief the shot flashed just wide.
Crowd pleaser Zaki was again involved as Wigan snatched a sensational lead after 16 minutes. He was fouled by Vincent Kompany and, having failed to deal with Olivier Kapo's free-kick, the ball ran to Antonio Valencia who smashed in an unstoppable shot from just outside the box.
City should have levelled a minute later when Stephen Ireland played Robinho in with a great ball but the ex-Real Madrid striker poked the shot wide with only the keeper to beat.
But the Brazilian touch of Robinho's fellow countryman Elano did the trick for City when he fired in a free-kick from the right, the Wigan defence was slow to react, and the equaliser went in off Belgium international Kompany.
The Latics were back in front after 34 minutes when Zaki claimed his sixth goal of the season with a controversial penalty after Wilson Palacios crashed to the floor when challenged by Javier Garrido as he chased Emile Heskey's ball into the box.
Ireland failed to take a shooting chance after being set up by Pablo Zabaleta but City were hunting another equaliser and Kirkland saved Wigan when he tipped one over the crossbar from Wright-Phillips.
Wigan came under heavy pressure after the re-start with Jo and Elano both just failing to hit the target for City and Ireland poked another effort wide after getting past Titus Bramble.
Kirkland came to the rescue again saving from Wright-Phillips and City's frustration grew when a penalty claim was waved away after Bramble and Micah Richards collided on the edge of the box.