What a contrast to earlier when they won their first nine home league games to occupy a Champions League spot for much of the early part of the season.
But this was a poor performance and City's season is in danger of petering out into a damp squib as they slip down the table.
Battling Wigan, meanwhile, picked up another valuable point in their fight to stave off relegation.
They also maintained their excellent record against City, who have failed to beat them in their last six Premier League meetings.
City had the better of the handful of scoring chances in a dismal goalless opening half.
Wigan keeper Chris Kirkland made an excellent early save to keep out a header from Darius Vassell following a left-wing cross from Michael Ball.
Stephen Ireland then curled a shot narrowly over the crossbar before turning provider to put Benjani Mwaruwari clean through on goal with an inch-perfect pass.
Kirkland again came to Wigan's rescue by racing from his line to bravely block at the feet of Benjani and in the process sustained a chest injury which needed treatment.
Wigan only managed a couple of attempts at goal, but Marlon King and Emile Heskey failed to trouble keeper Joe Hart .
City lost Brazilian Elano, who limped of with a knee injury minutes after the restart and then, shortly after the hour-mark, manager Sven-Goran Eriksson took off Ireland.
But the introduction of Ecuador international Felipe Caicedo and Mexican Nery Castillo failed to inspire City, who continued to labour as they rarely threatened to break down a well-disciplined Wigan defence.
City had a great chance to make a breakthrough in the 71st minute when Caicedo and Vassell combined to open up the Wigan defence, only for Benjani to shoot wide from six yards when it looked as though he could not miss.
Yet in the closing stages, Wigan had two great chances to snatch victory.
Heskey's hard work set up Wilson Palacios and the Honduran was denied by a super save from Hart, the first time the City keeper had been troubled all afternoon.
Then Jason Koumas and Luis Antonio Valencia linked well to set up substitute Antoine Sibierski, only fro the ex-City player to see his goal-bound shot blocked by City captain Richard Dunne.