Balotelli was due to face an automatic one-match suspension for accumulating four yellow cards when he was needlessly booked for failing to retreat at a free kick.
But Serie A's disciplinary commissioner said in a statement he had added another two matches after Balotelli's angry altercation with the match official at the end of the game. It was not clear what had upset "Super Mario".
It was awful timing by Balotelli as third-placed Milan's next two games are against second-placed Napoli and leaders Juventus as they try to wrap up the third and final Champions League spot.
Balotelli had previously managed to stay out of trouble since his move from Manchester City in January.
But his problems began on Saturday as the team travelled by high-speed train to the game in Florence and he was caught smoking in the toilet by a ticket collector.
Milan officials were told and Balotelli was fined.
So far, his misdemeanours have paled in comparison to his antics at Manchester City which included rash tackles and a incident where he set fire to his house after letting off fireworks in his bathroom.
"AC Milan would like to communicate that it will appeal against the three-match suspension handed out to Mario Balotelli," a statement on the club's website read.
The 22-year-old has made a major impact since returning to Italy, scoring 10 goals in 11 matches for club and country this year, but Milan got a taste for his more controversial side this weekend.
Chief executive Adriano Galliani told Gazzetta dello Sport Balotelli is also facing a club fine for smoking in the toilets on the train to the match.
- Sports & Recreation