The former Wolfsburg striker headed in the only goal of the game in the first half as the visitors pulled three points clear of rivals Manchester United at the top of the table
The visitors' only goal came in the 22nd minute courtesy of an Edin Dzeko header, his first in 11 appearances for the club, nodding in from a David Silva free-kick.
The hosts started the brighter of the two sides and they had the game's first chance inside the first three minutes - a James McArthur volley from the edge of the box that was deflected wide.
During that passage of play, Jordi Gomez was upended by Gareth Barry in the box but referee Martin Atkinson deemed it more of a coming together and immediately signalled that it wasn’t a penalty.
Dzeko then missed an easy headed chance to put the visitors one up as he sent his effort wide when he really should have done better.
Montenegro international Stefan Savic, in for the suspended Vincent Kompany, headed over after a short corner was eventually crossed into the box by David Silva.
Victor Moses ran at City’s makeshift defence, weaving in and out, before blazing over from 20 yards shortly after.
Dzeko, having been fouled by Antolin Alcaraz down City’s left flank, then popped up in the box to head Spaniard Silva’s out-swinging free-kick into the net to open the scoring.
Maynor madness | City players want Figueroa sent off for handball
It was a needless free-kick to give away as the Bosnian was going nowhere and the hosts paid the price, allowing the striker to notch his first in 11 appearances for the visitors.
McArthur made goalkeeper Joe Hart work from outside the area but the former Shrewsbury Town man was more than a match for the shot and held well.
City were phenomenal in closing the hosts down every time they got the ball and Samir Nasri almost capitalised after closing down in the Wigan area but the chance went begging.
There were times in the first half that the top versus bottom divide looked huge but the longer the hosts were just the one goal behind the more they were getting confident. They started spraying the ball around, looking for their own bit of space but just couldn’t find that final ball.
Sergio Aguero was on the end of Silva’s counter attack and he forced Ali Al-Habsi into a smart stop to keep the score down to just the one goal in the first 45.
The second half started the way the first did, with Roberto Martinez’s side flying out of the blocks and bombarding the City box.
McArthur wasn’t frightened to shoot and when given the opportunity he opted to strike from range and on 50 minutes he did so again but dragged his shot wide of Hart’s right-hand post.
A three-minute spell by City just before the hour mark should have at least doubled their lead.
Birthday boy Pablo Zabaleta set up Nasri who cut the ball across the box to find Dzeko. The Bosnian got the ball out of his feet before curling a delightful shot towards the top left-hand corner but Al-Habsi’s outstretched hand kept it out. He then got himself back up blocked Silva’s rebound to complete a brilliant double save.
Then almost immediately Aguero produced a piece of magic that even his father-in-law Diego Maradona would have been proud of. The Argentine took on four or five Wigan defenders and gradually worked his way into the box but before he could get his shot away, strike partner Dzeko nicked the ball off his toes and the chance came to nothing.
Just like the first half, the longer the 45 was going the more confidence Wigan were gaining and James McCarthy forced a stunning save from Hart, sticking his left leg out at the vital time to prevent the equaliser.
Al-Habsi again kept the scoreline down, smartly readjusting his body after Caldwell had blocked Dzeko's shot from range nine minutes from time before Aguero dragged his shot wide.
Maynor Figueroa was then fortunate to escape with just a yellow card as he stopped the ball with his hand on the half-way line with Aguero accelerating into the space behind the Wigan defender.
City were hanging on in the closing stages but they managed to keep their cool defensively and secured three vital points to send them clear at the top.
Follow the Premier League LIVE on Goal.com:
Commentaries, Stats, Player Ratings and much more,
Visit Goal.com Live Scores!