The Lega took action after the 22-year-old was subjected to "racially discriminatory chants" by a section of Nerazzurri fans at the San Siro, while several supporters were seen waving inflatable bananas towards the Italy international.
A statement published on Gazzetta.it confirmed that Balotelli has also been fined 10,000 euros (£8,600) for directing a vulgar gesture at the Inter fans when leaving the pitch at the final whistle, with Milan receiving a 10,000 euro fine for unveiling "insulting banners".
Inter were recently fined 20,000 euros (£13,200) when a section of fans were heard singing racist songs about Balotelli during a Serie A match against Chievo.
The Lega statement explained that Inter had been issued with the heavy punishment as certain fans were observed directing "shouts and chants containing racially discriminatory expressions to a player of the opposing side" on five separate occasions.
Inter also fell foul of the authorities for unveiling four separate banners insulting Milan players, with a laser pen being shone onto the pitch in the 75th minute.
Milan were also fined as fans unfurled a banner mocking their former striker Antonio Cassano, now with Inter, who had life-saving heart surgery while playing for the Rossoneri.
Balotelli was later praised by the management of both sides for keeping his cool during the match, which ended 1-1, but he was adjudged by the Lega to have directed an undisclosed insulting gesture towards the Inter fans as he walked towards the players' tunnel.
The events of Sunday's match marked the third time Balotelli has been the victim of racism since his return to Italy after spending two-and-a-half years in England with Manchester City.
Inter president Massimo Moratti apologised when a section of his club's fans sang racist songs about Balotelli during a league victory over Chievo, but Milan's own management had already made an embarrassing public blunder.
Milan vice-president Paolo Berlusconi - the younger brother of club owner Silvio - was filmed at a political meeting in Monza near Milan describing Balotelli as "negretto della famiglia" - translated as "the family's little negro".
That came just four weeks after Silvio Berlusconi praised midfielder Kevin-Prince Boateng for walking off the pitch after he was racially abused during a friendly against Pro Patria.
Tuesday's announcement follows news that Lazio could be facing the prospect of playing a home Europa League tie behind closed doors after UEFA charged the Rome club over the behaviour of their supporters for the fourth time this season.
European football's governing body confirmed it has charged the Rome club over the "racist behaviour" of their fans during last Thursday's 2-0 win over Borussia Monchengladbach as well as the "throwing of missiles and or fireworks" and "insufficient organisation".