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.
It was Balotelli's first Premier League goal of the season and came moments after a bad miss from the Italian and after Mancini opted to replace strike partner Sergio Aguero.
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."
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Balotelli was dropped for a match against Tottenham earlier this month and was then kept out by a back injury.
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."
Balotelli's future has been the subject of speculation in the recent weeks but Mancini - not for the first time - said a firm "no" when asked if he intended to move on his fellow Italian in the January transfer window.
Wigan caused City plenty of problems and had several good chances to take the lead before City finally broke through.
Arouna Kone put a headed chance wide before City broke and struck when Balotelli snaffled a rebound from an Ali Al Habsi save at the second attempt.
Mancini said: "We knew before the game it was difficult because every time we play against Wigan, we don't win easy.
"They play good football, their manager is a good manager and they play very well.
"We had some problems for various positions on the pitch, but I think in the end we deserved to win because we shot 16 times against one and we should be also passionate in this game."
Official statistics actually showed City had 15 attempts on goal to Wigan's nine.
Mancini also confirmed Milner, who spent just 21 minutes on the field before being forced off, had suffered a hamstring injury and will be assessed in the coming days.
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.
"We could have been more patient but the frustration is we couldn't find a goal. That was the only thing missing.
"But I loved the attitude, effort and personality that we showed. We kept showing that desire.
"It was a very pleasing performance from many aspects but we are still disappointed.
"I don't want to be a Wigan Athletic representative saying we are happy to lose with a good performance against the champions. That is not accepted any more.
"It is not good enough for us. We are disappointed we couldn't get a positive result."