Balotelli struck brilliantly in the 84th minute after two sucker punches from Luca Siligardi and Paulinho had turned the game in the home team's favour following the former Manchester City forward's seventh-minute opener.
Eighth-placed Milan, who were sloppy in defence and attack, now have 18 points from 15 games. Livorno are fifth from bottom on 13 points.
Balotelli came close to securing a barely deserved win for his side, hitting the bar with another spectacular looping effort two minutes from the end.
"That's football. Next time it will go in," he told Sky Sport Italia.
Balotelli has netted three times in his last two games to return to scoring form, perfect timing for Milan who are looking to rally from a miserable start to the season.
The former European Cup holders will need the volatile striker at his best for Wednesday's Champions League group decider with Ajax Amsterdam at the San Siro.
"I have always been in good shape and never had any of the problems that were written about me," said Balotelli. "I just wasn't scoring, that's all.
"We are playing fairly well and are scoring again at last, which was a problem before, so now we just need a little more luck."
Third-placed Napoli host Udinese in Saturday's late game hoping to close their nine-point deficit on leaders Juventus who beat Bologna 2-0 on Friday.
(Editing by Tony Jimenez)
