City came from a goal down to beat the defending champions 2-1 at the Estadio do Drago on Thursday, but the BBC reported that club officials had informed them that the two black players had been targetted by sections of the home crowd.
After the final whistle City manager Roberto Mancini said he had heard nothing unusual.
"I didn't hear the noise, because I was concentrating on the game," he said.
But it was claimed that after the game Balotelli had told a City official that he was subjected to racial abuse from the stands. The club then announced that they intended to report it to UEFA.
Mancini added later: "I didn't hear (any racist chanting), sorry."
"I think Mario Balotelli and Yaya Toure are too strong (to be affected by it)."
Toure confirmed he had "heard something" from the stands.
"That's why we all like the Premier League, because it never happens there," he told Sky Sports.
"Maybe in foreign countries they don't expect black players. I think in future it will be okay, they will change their minds and the game will become more open
"Football is football and the fans come to enjoy the game, and we don't want things like this to happen.
"Mario is now able to control things like this and that is very important for the club."