The center took a hit in the corner from Bruins defenseman Jarred Tinordi at 6:42 of the first period. Malkin remained on the bench before going to the locker room but returned to the bench at 12:29.
He participated in a power play that began at 13:13 of the first before leaving a second time. He did not play the remainder of Pittsburgh's 2-1 loss.
Penguins coach Mike Sullivan said Malkin was being evaluated but they had no other information.
"Nobody likes to see that," Pittsburgh captain Sidney Crosby said. "We don't know if it's going to be the rest of the game or a couple shifts. You're trying to push and make sure that whoever is out there sets up the next line for a good shift. I think you never like seeing any teammate get hurt and leave the game."
Tinordi left the game with 7:03 remaining in the second period after he was hit by Penguins forward Brandon Tanev, who was given a major penalty for boarding and a game misconduct.
Tinordi was helped off the ice with an upper-body injury. Boston coach Bruce Cassidy did not have an update on Tinordi but said his chances of playing against the Buffalo Sabres on Thursday were "not great."
Malkin entered with 12 points (four goals, eight assists) in an eight-game point streak after reaching 1,100 NHL points (424 goals, 676 assists) with a goal and an assist in a 4-1 win against Boston on Monday.
Malkin is one of four Penguins who have played in all 29 games this season. Forwards Bryan Rust, Jake Guentzel and Tanev are the others.
