Wigan Athletic were dealt a cruel blow with seven minutes remaining at the Etihad Stadium when Carlos Tevez scored with only Manchester City's second shot on target.
It was a performance to admire from Latics as they prevented the hosts from creating chances and had a Shaun Maloney effort cleared off the line.
Roberto Martinez made two changes from the side that beat Millwall 2-0 in the FA Cup semi final at Wembley on Saturday, as Franco Di Santo and Joel Robles came in to replace Callum McManaman and Ali Al Habsi.
The Etihad crowd was somewhat subdued in the early exchanges as Latics pressed from the kick off with excellent possession in the final third.
After an initial nervy spell for the hosts with Latics looking in control, the game started to open up as City attempted to unlock Latics in the wide positions.
It was to be Latics who found an opening out wide though, as Jean Beausejour opened up space on the left side, playing a low and flat ball into the area which forced Javi Garcia into slicing the ball over his own cross bar.
That chance came after 34 minutes of a chess-like game of football as both sides tried to work out each other's next move.
Moments later and quick thinking from a free kick halfway into City's area gave Arouna Kone a chance at the back of the penalty area.
The ball dropped down behind Samir Nasri and the Ivorian struck first time but fluffed his lines as the ball ricocheted off his standing leg.
Excitement was the buzz word for the final 10 minutes and end-to-end football broke out, starting with Latics' best chance of the game.
A fluid move which resulted in Shaun Maloney back heeling the ball into the path of Franco Di Santo on the edge of the area was almost finished off perfectly but for an outstanding save from Joe Hart.
Di Santo picked the ball up 18 yards out and fooled two Man City defenders with a drop of the shoulder, before shaping up to side foot the ball under Hart's body but, the England goalkeeper smothered the ball to save.
The hosts then countered and almost had a goal of their own when Carlos Tevez broke down the right hand side and played a low cross along the edge of the six yard box, fortunately for Latics everybody in the box missed the ball, including the in-coming Sergio Aguero.
It was a first half that ended with a clever piece of goalkeeping from Robles who tipped the ball out for a corner after Aleksander Kolarov's cross almost sneaked in at the front post.
The second half continued in the same way for Latics as they quelled any City pressure and started to unlock the defence.
Just four minutes in and it should have been 1-0 to the visitors when Maloney used a drop of the shoulder just inside the area down the left and whipped the ball beyond Joe Hart, only for Lescott to hack it away off the line.
A front three of Arouna Kone, Franco Di Santo and Shaun Maloney fueled by the creativity of Jordi Gomez was looking primed to pounce the longer the half went on and the introduction of McManaman for Di Santo only added to the threat.
City began to create chances of their own as the game entered its final stages, with half time substitute Edin Dzeko forcing Robles into an instinctive save with the tip of his boot.
One minute after Paul Scharner was flagged offside at a free kick which he headed onto the cross bar, Manchester City got their goal.
A second shot on target in the whole game came from Tevez as he avoided tackles from Gomez and Scharner on the edge of the area before skipping into the box and lashing the ball into the inside netting of Robles' right post.
Latics pushed to level but City defended in numbers and used the corners to play down the clock, claiming three points in a game which deserved at least a draw for Latics.