Italy midfielder Pirlo was rested for the goalless draw against Livorno at the weekend, coming on as a second-half substitute but failing to inspire his team.
"It is possible that the return of Pirlo will have repercussions on the rest of the team," Leonardo told a news conference.
"He is a master piece in our game, he can play in different positions on the pitch.
Leonardo would not say whether Brazilian Ronaldinho, who has been far from his brilliant best for the seven-times European champions this season, would start Tuesday's Group C game at the Stade Velodrome.
"We must not think of Ronaldinho as an individual. We must think of the team, that is what matters."
AC Milan last played Marseille in 1993 when the Provence side defied the odds to win the Champions League final 1-0 in Munich, Germany.
Marseille coach Didier Deschamps, who captained the French side that day, was in cautious mood.
"AC Milan have players with a lot of experience, who are used to playing in this competition," Deschamps told reporters.
Leonardo also warned his players against complacency.
"Marseille did not finish second in the French league by chance," he said. "They will be out to prove they have their place in the Champions League."
AC Milan midfielder Mathieu Flamini played for Marseille in the 2003-04 season.
"The city is all about football, the stadium is a boiling one," he said.
