Balotelli endured a largely frustrating night on his first start in six matches, but battled on and turned an evenly-fought Barclays Premier League match in the champions' favour with a 69th-minute strike. City went on to win 2-0 with substitute James Milner hitting a stunning second goal three minutes later.
Mancini said: "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. Mario is one of the four strikers, we have four top strikers. In this moment we have had some difficulty scoring goals like last year, but I think if we work we can change this."
Balotelli was dropped for a match against Tottenham earlier this month and was then kept out by a back injury.
Sergio Aguero, by contrast, had started the previous five and this came into consideration when Mancini made his substitutions.
He said: "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."
Wigan caused City plenty of problems and had several good chances to take the lead before City finally broke through.
Wigan boss Roberto Martinez felt his team had more than matched City and that the Kone miss was a vital turning point.
The Spaniard said: "From our point of view, I think we edged the game for 60 minutes. The disappointment is we couldn't get the first goal in that period. When you are just slightly ahead of the opposition you have to score and that (Kone) was a clear chance."