The 23-year-old was substituted in the 83rd minute of the game at the Stadio Angelo Massimino shortly after Milan had gone 3-1 up.
Balotelli - who scored Milan's second goal on Sunday with a superb free-kick - was clearly agitated after having multiple run-ins with Catania defender Nicolas Spolli.
Widespread reports in the Italian media have since claimed the former Inter and Manchester City man was subject to a racial slur from the Argentinian, but Milan coach Massimiliano Allegri was unaware of any such incident.
"It was a fair game, I don’t think anything happened,” he told Sky Sport Italia. "Balotelli was a little tense and I preferred to remove him from the game, especially as were 3-1 up and he needs to rest."
Catania manager, meanwhile, Luigi De Canio feels there must have been a misunderstanding, adding that Spolli would not engage in such abuse.
"Spolli is a good man, so I think it must’ve been a misunderstanding," he said.
Milan came from behind to end their five-game winless streak at the Serie A bottom club, with goals from captain Riccardo Montolivo, Balotelli and Kaka overturning Lucas Castro's early opener for the hosts.
