Balotelli lifted a dreary match with his 10th league goal of the season, an incredible looping long-range strike from near the touchline in the 86th minute moving Milan up to 10th, level on 32 points with ninth-placed Lazio.
"I saw the keeper was off his line so I thought I'd try and hit it hard. Luckily for me I struck it well," said Balotelli.
The Italy striker cried after being substituted in last week's 3-1 defeat at Napoli and did not celebrate after his incredible winner on Friday.
"There's a tendency here to look too much at people's private lives and I would suggest that we avoid that because I'm an attacker in the national team. Leave me alone to live my life and give my best on the pitch," said Balotelli.
They remained four points clear of the relegation zone in 16th but on another night might have snatched a shock win with Jonathan Cristaldo unlucky not to score with a smart volley on the hour.
With chances at a premium the most interesting thing to happen in the first half came when referee Mauro Bergonzi suffered a bleeding lip after the ball deflected from a tackle between Riccardo Montolivo and Diego Perez and hit him in the mouth.
Bologna looked dangerous on the break and it took a moment of magic from an otherwise disappointing and seemingly disinterested Balotelli to grab a third win in five league games for new coach Clarence Seedorf.
With a place in next season's Champions League 15 points away, Milan will hope their local rivals slip up in Florence and that Hellas Verona, who are level on 36 points with Inter, stumble at home to fellow European challengers Torino on Monday.
The win is a boost for Seedorf as he prepares for Wednesday's home game against Atletico Madrid in the last 16 of the Champions League.
"Atletico do not play the same way as Bologna who defended very deep," said the Dutchman who also hit out at media reports that suggested he criticised Balotelli by saying that he "isn't a champion".
"People like to take what I say out of context. I didn't say Mario isn't a champion but that he will become a champion," explained Seedorf.
"I believe in him a great deal and I believe in the man he is becoming."