The striker received a second yellow card for protesting after the match at the San Siro was over and his ban has been extended for "intimidating and insulting remarks" toward the referee over his dismissal.
The Italy international will now miss the game against Bologna, Sampdoria and, perhaps most crucially, Juventus.
Milan can appeal the punishment.
Balotelli was heavily involved in the match against Napoli, missing a penalty for the first time in his career as Pepe Reina saved his spot-kick.
The former Manchester City frontman did score late on with a fine curling effort, but it was no more than a consolation.
The loss left Milan eight points behind leading pair Napoli and Roma after only four games of the new season.