The Italian hit his first goal in the Barclays Premier League since March to turn an evenly-fought clash against Wigan at the DW Stadium in City's favour after 69 minutes. City went on to win 2-0 after substitute James Milner struck a superb second goal three minutes later before leaving the field injured.
Balotelli had been making his first start in his six games and his first since being dropped by manager Robert Mancini for his attitude in training ahead of the clash with Tottenham earlier this month. Since then the Italian has been troubled by a back injury and he endured a largely frustrating night on a cold night in Wigan, including missing a simple headed chance, before his decisive goal.
Ali Al Habsi was unable to hold a low shot from Gareth Barry and Balotelli reacted quickly to smash in the rebound at the second attempt.
Mancini said of Balotelli: "I am very happy for him because he scored his first goal this year. He scored an important goal. I hope he can improve in the next week and the next game.
"We thought Mario or Sergio but Mario in this moment is maybe more fresh than Sergio. Sergio has played all the games and for this reason we changed. Also Mario moved well. He didn't play like he knows but in this position Mario was better in this moment."