The Italy international, who bagged the second goal of the Rossoneri's haul at the Stadio Angelo Massimino, appeared to be involved in a series of heated exchanges with defender Nicolas Spolli throughout the second half, prior to being subbed for being "a little tense".
Reports emanating from Italy have since suggested that the former Manchester City forward was the subject of a racial slur by the Argentine, but Allegri does not believe that this was the case.
Speaking to Sky Sport Italia, the coach said: "I don't think anything happened.
"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."
Meanwhile, Catania boss Luigi De Canio has also moved to defuse the tension, claiming that the incident was borne out of a "misunderstanding".
He added: "Spolli is a good man, so I think it must've been a misunderstanding."
The Italian giants, who went into the clash having failed to secure a victory in any of their last five Serie A fixtures, were forced to come from behind in the clash after Lucas Castro opened the scoring on 13 minutes.