By FOX Sports Staff
Referee Gianluca Rocchi suspended play between the two sides shortly after half-time when sections of Roma fans directed racist abuse at Balotelli.
"There's no point in interepting the game. It's a middle ground decision and it serves no purpose," Allegri said at his post-match press conference.
"Either the game should be suspended or you keep playing. Mario gave all he had this evening, but he's 22 years old and always subject to these racist boos and that's not good.
"People go to the stadium to watch the two teams but there's always these uncivilised people."
Tension between both camps did not help the situation on Sunday with two players sent off.
Sulley Muntari stupidly earned himself two quick yellow cards in the second half for refusing to accept Rocchi's decision to book Balotelli for an innocuous foul.
"Sulley made a mistake but it's in the past now. He's mortified and it was a blow playing the game with 10 men," Allegri said.
Roma failed to make their extra-man count and they themselves were reduced to 10 men when captain Francesco Totti was caught elbowing former team-mate Philippe Mexes.
Fiorentina's 1-0 win over Palermo on Sunday means the race for the final UEFA Champions League spot in Serie A will go down to the wire.
Third-placed Milan hold a two point lead over fourth-placed Fiorentina with one game remaining.
Allegri's side are away at Siena in their final game while the Florence-based outfit make the trip to Pescara.