Roberto Mancini's side remain just a point behind Manchester United, who beat West Ham at Old Trafford, but were made to work for the win over Wigan.
The home side almost took the lead through Arouna Kone in the first half but his header was well saved by Joe Hart, while weekend hat-trick hero Jordi Gomez saw a penalty appeal turned down before half-time.
City came out all guns blazing for the second-half and Balotelli should have put them ahead when he steered a header wide from close range.
Kone also failed to hit the target with a header at the other end and Roberto Martinez's side will rue the miss which came during a good spell for the hosts.
City scored against the run of play on 69 minutes when Gareth Barry's shot was spilled by Ali Al-Habsi and Balotelli scored on the follow-up, his first Premier League goal of the season.
The visitors doubled their lead three-and-a-half minutes later when substitute James Milner found the top corner with a stunning 25-yard strike.
The two goals were enough for the Champions who had failed to score in their two previous away league games and they have now won their last six meetings with Wigan without conceding a goal.
The Latics stay in 15th despite the defeat, two points above the relegation zone.