The Rossoneri coach believes this is the best time for the 22-year-old to showcase his quality and be a leader after his double gave Milan impetus to push for second place
The Italy international netted a first-half penalty before adding another midway through the second half as the Rossoneri kept within touching distance of second-placed Napoli, who secured a 3-2 win over Atalanta at the Stadio San Paolo.
Balotelli has now scored seven goals since his high profile return to Italy and Allegri believes his youthful Milan side led by the former Manchester City forward can be the platform the striker needs to showcase his talent.
"I think it's an important opportunity for Balotelli, as for the first time he is the protagonist in a team full of youngsters," Allegri told reporters after the game.
"He is relaxed and an excellent professional. He has been on the European stage for seven or eight years, but this is his best chance so far to really show his qualities."
The Milan coach was also quick to play down reports of a rift between himself and striker Stephan El Shaarawy, who stormed down the tunnel following his second-half substitution.
"Stephan El Shaarawy is having an extraordinary season that nobody expected, so it's only normal he will have a slight dip in form," Allegri added.
"He played well today and almost scored a goal, but at that moment I needed fresh legs.
"He needs to relax, as he is doing so well and his performances help the team just as much as goals."
Allegri's contract only runs until the summer of 2014 and speculation has been rife that he might leave San Siro, but the Italian refused to discuss contract issues after the Palermo game.
"I have a contract until 2014, and the president has expressed kind words about me," he added.
"Meanwhile, I want to second place, and even if we finish in the top three then that would be extraordinary."