It was City's fourth successive Premiership loss which leaves them only one place above the bottom three.
And City, unbeaten at home in the league until December, have now suffered five losses in their last six Premiership games at Eastlands.
The latest loss was inflicted by Caleb Folan, a striker who until January was plying his trade with Chesterfield in League One.
Folan, a £500,000 capture, struck his second goal for Wigan which made it ten points from a possible 15 to considerably ease their own troubles.
And the victory enabled Wigan to maintain their 100 per cent Premiership record against City, having won all four of their meetings.
Wigan could have taken a tenth minute lead when Lee McCulloch hit a shot into the ground and had the misfortune of seeing it loop over the crossbar.
And it was no surprise when the visitors, on top in the early stages, took the lead eight minutes later from a Leighton Baines free-kick.
Emile Heskey headed the ball high back across the face of goal and Folan nodded it high into the roof of the net from a couple of yards having escaped his marker.
The unlucky McCulloch went close again with a drive from 25 yards which keeper Nicky Weaver tipped around the post for a corner.
City's troubles increased when Michael Ball and Hatem Trabelsi were booked in quick succession.
Ball was fortunate not to concede a penalty as television replays indicated he fouled Luis Antonio Valencia inside the box, but referee Howard Webb gave the free-kick outside.
City were completely out-played for the opening half-hour and disgruntled fans demanded to know what was going on.
It was only late in the opening period that City began to make any headway.
Twice in the space of three minutes defender Richard Dunne went close, each time with headers from Joey Barton corners. On the second occasion his goalbound effort was blocked by Emmerson Boyce.
City brought on Emile Mpenza at half-time for his first appearance as he replaced the ineffective Georgios Samaras.
And Belgium international Mpenza nearly made it a dream debut as within four minutes he almost scored, failing by inches to connect with a left-wing cross from DaMarcus Beasley.
A rare mistake by City defender Sylvain Distin let in McCulloch, but goalkeeper Weaver managed to keep out his long-range shot.
City continued to huff and puff but rarely threatened the Wigan goal. Barton had a great chance, but shot weakly at goalkeeper John Filan, who then made a decent block with his legs to deny Beasley.
The City fans had become so disillusioned that they were leaving the ground in their droves with 15 minutes still remaining.
Those who remained voiced their disapproval with chants aimed at manager Stuart Pearce of 'Psycho, Psycho sort it out'.
Pearce's response was to send on 17-year-old striker Daniel Sturridge for the last four minutes in a desperate bid to salvage something from the game.
But with City committed to all-out attack, Wigan almost scored a second goal deep into stoppage time.
Weaver's poor clearance found substitute Kevin Kilbane, but he was denied by a brilliant save from the keeper, who atoned his error.