Balotelli endured a largely frustrating night on his first start in six matches, but battled on and turned an evenly-fought 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.
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.
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, including a Arouna Kone header which edged wide, before City finally broke through.
Oman goalkeeper Ali Al Habsi was unable to hold a low strike from Gareth Barry's land Balotelli was quick to react. His first effort was blocked, but he made no mistake in tucking away the second.
City put the result beyond doubt just three minutes later as substitute Milner, brought on for the ineffective Javi Garcia, found the top corner with a stunning long-range strike.
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."
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.
Roberto Martinez, the Wigan manager, felt his team had more than matched City and that the Kone miss was a vital turning point.
"From our point of view, I think we edged the game for 60 minutes," he said afterwards. "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."
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