Balotelli, when not suspended, has been a regular starter since joining Milan in January but found himself shunted out of the starting line-up at the Nou Camp on Wednesday as Allegri decided to start with Kaka and Robinho instead.
Allegri, once again fighting to keep his job after a dismal run of results and performances, hinted after the game that he was longing for the return of injured striker Stephan El Shaarawy and that Balotelli was struggling to keep up.
"Balotelli was a reserve at both Inter (Milan) and Manchester City, this is the first time he has been a regular first team player at a big club," he told reporters.
"He hasn't played very well in the last few games and has been recovering from the injury he suffered with the national team, so I preferred to start with the Kaka-Robinho combination.
"Of the 18 players we had tonight, none had El Shaarawy's characteristics," he added.
"Balotelli is not a problem, and he did very well when he came on at halftime. He has extraordinary qualities but he has to improve in the context of the team.
"He's just not used to playing every three days. We need everyone, all the players are important."
Despite their unhappy run, Milan are still second in Champions League Group H with five points from four games and matches against Celtic and Ajax Amsterdam, the two teams still below them, still to come.
Their defeat on Wednesday, which extended their winless run to five matches in all competitions, had been entirely expected but it will be different on Sunday when they visit lowly Chievo in Serie A.
"From now on, we have to think about getting results," said the phlegmatic Allegri, who led Milan to the Serie A title in his first season in 2010/11 but has struggled in the last 18 months.
"The coach always depends on results but it is the club who will judge me.
"On Sunday, we will have to battle, it will be a different type of game. I'm not worried, like everyone else I want to win a match."
- Sports & Recreation
- Stephan El Shaarawy