Balotelli, replaced by Samuel Eto'o at half-time, headed home a corner in the 42nd minute after Bologna's Marcelo Zalayeta had cancelled out Diego Milito's opener for the champions.
Esteban Cambiasso drove home a diagonal strike in the 72nd to seal a win that gives Inter 32 points from 13 games.
Balotelli has been criticised several times recently for his attitude by Mourinho, who gave the 19-year-old a mark of "close to zero" for his performance in Inter's 1-1 draw with AS Roma before the international break.
"We won well, without any problems, we deserved it," Mourinho told Sky. "Mario had a normal first half. He missed one chance but he scored another," said the coach, adding he brought him off to avoid the risk of a red card after he was booked.
Later on Saturday forward Davide Lanzafame sprinted onto a long ball and coolly slid in Parma's winner in the 67th minute.
Fiore's Marco Donadel was given a second yellow card four minutes from time for a dangerous challenge with both feet.
