In a match devoid of clear-cut chances, the Italy international wowed the home fans at San Siro with a stunning 35-yard effort that flew into the top corner in the 86th minute.
The result was harsh on a Bologna side who had limited the hosts in front of goal for the majority of the match, and themselves had chances to claim the points through Jonathan Cristaldo and Lazaros Christodoulopoulos.
But Balotelli's moment of brilliance secured all three points for Clarence Seedorf's below-par side.
The former Inter and Manchester City man confessed Milan - who now sit ninth in Serie A - had underperformed, but he wants to be the man to guide them up the table.
"I looked at the goalkeeper and saw he was a little off his line, so I hit it with full force and fortunately it went in," Balotelli told Sky Sport Italia.
"It's a good goal. The coach gives me confidence, as I am the one who has to pull the team forward and therefore it's my duty to score these goals.
"It wasn't a great game tonight, anything but."
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