The 44-year-old revealed that the Brazilian attacker is suffering from pain in his lower back, and could miss Sunday's trip to the relegation-threatened side
The 22-year-old scored the winner in extra-time to book a clash with Lazio in the quarter-finals, but Allegri revealed that the forward had suffered an injury during the game.
"Pato felt some pain in his lower back and the medical staff will look at him tomorrow [Thursday]," he said.
"We play against Novara again on Sunday but we have time to rest."
Allegri was buoyed by the character shown by his side and also the performances of the returning Alexander Merkel and Stephan El Shaarawy, who scored the Rossoneri's opener.
"I was disappointed that we had to play 120 minutes of football," the former Cagliari boss confessed.
"We could have closed the game out earlier but the players did well to get through it in the best way possible. Winning the way we did will help the team.
"Merkel had a good game. El Shaarawy played well and has grown a lot, especially in the last two months and he’ll definitely do well."