Lee McCulloch's second half header gave Latics their second double of the season.
Manchester City became the second club in the Premiership to lose twice to Latics in the league. City were only three points behind Latics before this encounter, and Everton's win over Aston Villa made it even more important for either club to get a win today as the race for a European spot becomes even more intense.
Stuart Pearce's men were due to play West Ham in the F.A. Cup just 48 hours after today's match, and therefore the Blues boss decided to make eight changes. Latics boss Paul Jewell kept the same side that won at Sunderland last week, which meant Jimmy Bullard made his 200th career start.
It was a scrappy start at the City of Manchester Stadium and both sides struggled to find any rhythm to their passing. But Latics had a glorious chance but failed to take advantage of City's defensive error.
In the 13th minute Danny Mills' poor clearance deflected off Jason Roberts, and the ball was also poorly dealt with by David Sommeil. It fell perfectly into the path of Henri Camara who raced into penalty box before striking, but the ball went over the bar.
But Latics were very fortunate not have gone behind in a bizarre incident seven minutes later. After Filan caught the ball from a corner, he threw the ball out of the box, but it bounced back of Distin's head, and the Australian 'keeper watched the ball rebound off one the posts of his own goal! Thankfully referee Martin Atkinson blew his whistle for a foul on Distin for obstruction.
City made an early substitution with Greek striker Georgias Samaras replacing Antoine Sibierski after just 26 minutes.
Within seconds of the substitution, Latics went on the counter attack and Gary Teale struck a loose ball from twenty yards, but David James made a great save to deny Latics.
And Latics went forwards again just moments later as Leighton Baines easily passed Danny Mills before cutting into the penalty area. He tried to play in Roberts, but it was a poor decision as James easily gathered up the ball.
Wright-Phillips deservedly received a yellow card just after the half hour for a reckless challenge on Leighton Baines, as the defender played a clever pass through to Kavanagh.
City squandered a chance when Bradley Wright-Phillips flicked the ball over himself inside the box, but Samaras was indecisive and just passed it into the hands of Filan.
The home team were denied the lead by a brilliant save by Filan just minutes before the end of the first half. Leighton Baines clattered into Stephen Ireland and conceded the free-kick. Ireland's well taken set piece was flighted into the penalty box and had to be tipped over the bar by Filan.
And then moments later the action reverted to the other side of the pitch as Lee McCulloch headed wide from a Jimmy Bullard corner
After a slow start to the first half, it was pretty even for both teams in terms of clear cut chances although City looked to have seen more of the ball.
Half-Time: Man. City 0 - 0 Latics
City were literally inches from taking the lead six minutes after the restart, although it is debatable whether a goal would have been allowed anyway. Stephen Ireland's corner was punched by Filan, although the Australian goalkeeper had Wright-Phillips backing into him! The ball was then headed off the line at the far post by Baines.
But Latics themselves went better with their corner and did take the lead on 55 minutes through Lee MCCULLOCH. After David James made a hash of an attempted clearance, he had to leave it to his defence to put the ball out for a corner. The Latics midfielder easily headed home at the far post from Jimmy Bullard's well taken corner.
Stuart Pearce found himself having to take off substitute Georgias Samaras due to a suspected ankle injury, and Ishmael Miller came on just after the hour mark.
The goal seemed to boost Wigan's confidence, and displayed more confidence with their passing movements. But City equally looked threatening as when they came forward.
Bullard tried his luck in the 76th minute with a spectacular half-volley from thirty yards , the ball dipped towards goal, but it was a pretty easy catch for James.
Stuart Pearce's men had a chance to level the scores in the 79th minute when Chimbonda tackled Ishmael Miller to concede the corner. Sun Jihai was the man who took it and the ball eventually fell to substitute Lee Croft, but the youngster fired wide of the target.
City were desperate to find an equaliser and at the end of normal time Trevor Sinclair raced down the right flank before cutting into the penalty. The England winger fired a low shot, but Filan caught the ball at the second attempt.
Jason Roberts should have doubled the lead in stoppage time as he found himself one-on-one with David James, but the Grenadan's shot was deflected off the body of the huge England goalkeeper, and it went out for a corner. It was an unbelievable miss from the Latics striker, but also a good save by the 'keeper.
Latics kept their composure to see out the game until the final whistle, and these three points could prove to be very important as Jewell's men try to keep up for a place in the UEFA Cup next season.
Full-Time: Man. City 0 - 1 Latics
Latics Starting Line-Up: Filan, Chimbonda, Baines, De Zeeuw (c), Scharner, Bullard, Kavanagh, Teale, McCulloch, Roberts, Camara (Johansson 85).
Unused Substitutes: Walsh, Jackson, Thompson, Ziegler.
Manchester City Starting Line-Up: James, Sommeil, Thatcher, Distin ©, Reyna (Croft 66), Sibierski (Samaras 26 (Miller 61)), Sun, Mills, Sinclair, Ireland, Wright-Phillips.
Unused Substitutes: Weaver, Richards.
Referee: Martin Atkinson (West Yorkshire)
