The controversial forward began his career with the Nerazzurri but joined their arch rival from Manchester City during the January transfer window, much to the anger of Inter supporters.
"Balotelli did very well not to react to the provocations, I'm just sorry he wasn't able to score," Allegri praised after the game.
Nerazzurri fans were at the center of controversy earlier this month when they launched racist chants about the Italy international in the wake of his move to Milan, resulting in a 15,000 euros fine for the club.
Before Sunday's game, president Massimo Moratti and Inter 'ultras' released statements warning against a repeat of those actions.
The warnings over racism were generally heeded though abusive personal banners aimed at Balotelli were on show at San Siro.
Some Inter fans waved inflatable bananas, items which have become a regular sight at Serie A games and not considered to be a representation of racist abuse.
The 22-year-old has scored four times in as many games for the Rossoneri since joining the club.