Malkin injured his right knee Friday in a collision with Buffalo's Tyler Myers. Examinations indicated torn anterior cruciate and medial cruciate ligaments in the knee. Surgery was set for Thursday and recovery will take about six months.
The team said Malkin is expected to rejoin the Penguins in September training camp.
Malkin, who won the 2009 Conn Smythe Trophy as the most valuable player in the playoffs, had 15 goals and 22 assists in 43 games this season. He was the 2007 NHL rookie of the year and led the league in scoring in the 2008-09 season, which ended with the Penguins winning the Stanley Cup.
Pittsburgh is also missing leading scorer Sidney Crosby, who has been out of the lineup for 14 games since suffering a concussion early this year. Team officials said they are unsure when Crosby might return to the ice.