Massimo Moratti's side will pay €15,000 [£12,900] after the AC Milan man was the subject of offensive songs during the Nerazzurri's 3-1 victory over Chievo on Sunday
The former Manchester City man, who previously played for Inter before moving to England in 2010, joined rivals AC Milan during the January transfer window.
It is the second high-profile case of racism involving Balotelli since the striker returned to Italy.
Paolo Berlusconi - the brother of AC Milan president Silvio - was filmed using offensive language when referring to the Italy international prior to his debut against Udinese.
Earlier in the season, Milan midfielder Kevin-Prince Boateng left the pitch during a friendly with lower league side Pro Patria after being subjected to racist abuse by supporters.
Meanwhile, Juventus were also fined for offensive songs sung about rivals Napoli, who were also ordered to pay the same amount after a laser pen was used on a referee during a clash with Lazio.
Nerazzurri supremo Massimo Moratti blasted the behaviour after the match and has warned that the actions cannot be repeated when the Milanese rivals meet on February 24.