David Silva was the recipient of a remarkable spill in the 37th minute as his harmless shot went through the Oman international's legs . The result kept City in the Champions League qualifying spots as an out of sorts display infuriated manager Roberto Mancini.
For City, the return of Vincent Kompany from injury softened the blow of centre-back Kolo Toure's suspension for a failed drug test. The Belgian was one of two changes to the team that defeated Aston Villa 3-0 in the F.A. Cup on Wednesday, with top scorer Carlos Tevez also included as Jerome Boateng and Aleksandar Kolarov were demoted to the substitute's bench.
Latics boss Roberto Martinez made two alterations to the side that slumped to a 4-0 defeat to Manchester United last weekend. Right-back Adrian Lopez was handed his first Premier League start in place of Steve Gohouri, while Charles N'Zogbia made way for United loanee Tom Cleverley.
After scoring performances in two successive games, City attacker Mario Balotelli was the first to threaten in the third minute. An excellent clearance from Joleon Lescott on the stretch from a Maynor Figueroa cross set up a counter-attack which led to the Italian's powerful shot from the left of the penalty area being unconvincingly pushed away - in a sign of things to come - for a corner by goalkeeper Ali Al Habsi.
Martinez took his usual spot on the touchline as he attempted to orchestrate his struggling sides' play. The Spaniard had cause to worry again in the ninth minute as only a mis-control from Gareth Barry inside the box prevented another opportunity for the hosts following a delightful one-two with David Silva.
Referee Staurt Atwell took the centre of attention in the 16th minute as right-back Micah Richards crunched into Cleverley at top speed on the half-way line. The challenge was late and reckless, but the official was correct not to listen to the noise from the travelling support and issue just a caution.
With Richards' stud marks still fresh in Cleverley's leg, City twice went close to opening the scoring in the 23rd minute. Tevez, first, collected a Kompany pass 30-yards from goal and ducked his left shoulder to evade Mohamed Diame and dribbled past Antolin Alcaraz, but his shot was dragged just wide of Al Habsi's right post.
From the subsequent goal-kick, Wigan surrendered possession on the half-way line. Silva - who had already threatened in his usual pocket in-front of the opposition defence - could only shoot off the mark again from just outside the area when he had time on the ball to the frustration of the Eastlands fans.
Wigan had largely been under the cosh from the hosts but were gifted an opportunity to take the lead in the 29th minute. A jinking run from Victor Moses on the right of the City box produced a harmless low cross that was poorly stabbed into James McCarthy's path by Kompany, but the 20-year-old sidefooted wide of Joe Hart's goal from just eight-yards.
While Wigan turned their noses up at a present, City soon took the lead from one in the 37th minute. Silva was the benefactor as a calamitous spill from Al Habsi allowed the Spaniard's low shot from the left of the area to somehow spin through his legs much to his embarrassment and Martinez's frustration.
The Oman international's mistake was the last thing Martinez needed for his bottom placed side. The Spaniard watched on with arms slumped to his side in the final moments of the first half.
Wigan should have been deflated by Silva's goal but they took the game to City from the off after the interval. At Martinez's urging, bodies were finally thrown forward to support lone striker Hugo Rodallega.
This new enterprise was inches away from being rewarded in the 49th minute. After a sustained period of pressure, an outswinging corner from Ben Watson was met by Alcaraz, but the Paraguayan's sidefooted effort rebounded off Hart's left post with him and Pablo Zabaleta beaten.
Wigan were again denied on the hour mark as McCarthy produced a stunning save from Hart. The ex-Hamilton midfielder hit a stinging half- volley from the edge of the box from a knockdown from a long free-kick which was only half-cleared by the hosts.
While City had looked composed and Wigan toothless in the first-half, the script was turned around after the break. Holding midfielders Gareth Barry and Patrick Vieira bore the worst of Mancini's ire from the sidelines as they continued to give away possession and fail to kick into a higher gear when asked to win the ball in midfield.
City's enterprise seemed to have been left in the dressing room. Indeed, it took until the 76th minute for them to threaten a second goal.
Substitute Kolarov forced the chance as his cross was nodded into Silva's path by Caldwell on the stretch. The goalscorer but all his weight behind his effort from 20-yards but the skipper was quick to his feet and again put his head in the way of Al Habsi's goal.
Mancini's afternoon should have been made even more uncomfortable on the stroke of injury-time. Sloppy play again from City saw Latics substitute Conor Sammon tackled on the edge of the box.
The ball then made its way to Rodallega but his weak effort was stopped easily by Hart. The lack of conviction in the shot summed up Wigan's display, as with more desire they could have secured a share of the points.
Moments later, hearts were in the City support's mouth as even better opportunity was spurned by Sammon. The Irishman raced onto a Rodallega through ball, but under pressure from Lescott, he screwed his attempt wide from close range.
The shot was the last of a match which Wigan shouldn't have come away from empty handed. However, toothles finishing and error-strewn defending again left the Latics at the foot of standings and four points from safety.