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.
Promoted Parma moved up to third with 23 points courtesy of a breathtaking 3-2 victory at Fiorentina.
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.
Balotelli, an Italian of Ghanaian descent, celebrated his goal by raising his finger to his lips and commentators on Sky TV suggested the reaction was probably in response to racist chants from a section of the home crowd.
Before scoring Balotelli wasted a glorious chance when his hesitation allowed Bologna goalkeeper Emiliano Viviano to close him down before he shot.
"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.
Inter had bad luck with the score at 1-1 when a Dejan Stankovic strike hit one post and then the other before Viviano scrambled to the ball, while Milito rattled the bar before Cambiasso nailed their third goal.
They had full-back Maicon sent off in stoppage time, apparently for dissent.
Later on Saturday forward Davide Lanzafame sprinted onto a long ball and coolly slid in Parma's winner in the 67th minute.
Italy forward Alberto Gilardino had nodded Fiorentina ahead in the first half and then used his head again soon after the hour to equalise after the visitors had taken the upper hand with goals by Nicola Amoruso and Valeri Bojinov.
Fiore's Marco Donadel was given a second yellow card four minutes from time for a dangerous challenge with both feet.
