Balotelli was cautioned by referee Daniele Doveri for unsporting behaviour after scoring an 87th-minute equaliser in Sunday's game, which Clarence Seedorf's men went on to win 2-1 thanks to Giampaolo Pazzini's late header.
The booking will see Balotelli miss Milan's next Serie A match at home to Torino through suspension, and he was fined for a similar incident against Inter in February last year.
However, Prandelli, who coaches the former Manchester City forward at international level, insisted Balotelli still has his full support, while also praising the way new Milan coach Clarence Seedorf handled the situation.
"Balotelli will learn. He will need much love, he is a guy who we grant much to and who for Milan is important," the 56-year-old told reporters.
"I believe that Seedorf has said the right things and that with his help we can pull out the good things that Mario has inside.
"With Balotelli, Seedorf has used the right words. I'm not sure if he will have a lot of patience for him, but definitely a lot of love, because he is a boy who we hold very dear.
"Will he never learn? He will learn, he will learn."