The Italy forward was due to start the game on the bench, but Giampaolo Pazzini picked up an injury in training, which meant the 22 million euro January signing started the game on the pitch.
He scored after 25 minutes to put the Rossoneri ahead, but a goal from Giampiero Pinzi looked to have settled the game as a draw. However, a late - and very controversial - penalty was awarded and the striker calmly put away the spot kick to secure a stoppage-time victory.
Balotelli told reporters after the game: "I was supposed to be on the bench and Pazzo [Pazzini] was meant to play but he had a problem. I played from the start and it went well."
The former Inter starlet admitted that his fitness needs a lot of work, however, but exclaimed his joy despite his post-match exhaustion.
"I'm happy even if the game was difficult," Balotelli added. "I’m strong but my legs are still heavy. I haven't played many games and I have to train a lot."
The win leaves the Rossoneri level on points with archrivals Inter, and fourth in Serie A.