The three racism incidents have underlined Italy's serious problem with discrimination in soccer, which shows no sign of being eradicated despite renewed efforts from the authorities.
Serie A said in a statement on Monday that Roma would also have to close the Curva Sud section of their stadium for one game at the start of next term after the abuse during their clash with Napoli.
The statement said Inter, already fined 50,000 euros ($64,300) for racist chants towards Balotelli in February, had only been punished with the same fine for abuse at their game with Udinese but with a warning over their fans' future conduct.
Balotelli, who made his name at Inter Milan as a teenager and is famous for his idiosyncratic antics on and off the field, has been a long-time target of racist abuse in Italy and moved to England's Manchester City partly to get away from the hatred.
The Italy striker returned to AC Milan in January and has been a big success, scoring a controversial late penalty on Sunday which helped Milan win 2-1 at relegated Siena and take third spot and a Champions League playoff berth off a furious Fiorentina.
As Milan's team bus passed through Florence on its way back from Siena in the early hours of Monday, a group of Fiorentina fans shouted racist abuse, prompting Balotelli to take to Twitter to complain.
Milan's Kevin-Prince Boateng was praised throughout the game for walking off the pitch when racially abused by fans of Italian lower league side Pro Patria during a friendly in January.
But Italian Referee's Association president Marcello Nicchi said last week that Balotelli would be sent off if he were to leave the field to protest racist chanting.