But they were grateful - and relieved - to leave the DW Stadium with a share of
the points.
Charles N'Zogbia's stoppage time strike gave Wigan the half-time advantage just seconds after the Frenchman had one ruled out by referee Alan Wiley.
The ex-Newcastle star pounced after City's skipper for the day Shay Given had kept out the shot from Hugo Rodallega after good build-up work involving Paul Scharner and Jason Scotland.
It was his first of the season and made up for that earlier disallowed effort when Mr Wiley controversially blew up for a foul on Gareth Barry.
N'Zogbia had figured in a positive Wigan start, showing his willingness to shoot on sight and twice just missing the target.
Republican of Ireland star Given did well dealing with his first real test, a dangerous swerving shot after Rodallega let fly.
City had their moments with Shaun Wright-Phillips just beaten by an offside flag and Chris Kirkland doing just enough to keep out Emmanuel Adebayor after a terrific 50-yard ball from Carlos Tevez.
The Latics were good value for their 1-0 half time lead after the clearance from Titus Bramble was nodded on by Scharner and then touched to Rodallega by the hard-working Scotland, before N'Zogbia provided the finish.
But Wigan were caught cold within 90 seconds of the re-start when Tevez crossed from the right and Martin Petrov's trusty left foot did the rest.
Bramble then came to the rescue with a perfectly timed tackle on Adebayor and Wright-Phillips had a shot deflected over the bar.
Wigan missed a chance after a shooting mix up between Scharner and Rodallega and Kirkland - who needed treatment for a dislocated finger - kept out a Barry header.
City found themselves man down after 76 minutes when Zabaleta got his second yellow for the foul on Scotland.
Wigan almost cashed in when Mohamed Diame was just a whisker away with a superb effort and Hendry Thomas had one ruled out for offside.
Maynor Figueroa was fortunate not to concede a penalty for his tackle on Wright-Phillips, but City were again indebted to Given who pulled off late saves from Jordi Gomez and Rodallega as the Latics chased maximum points.