Penguins star Sidney Crosby also is a scratch for the game because of a concussion.
Malkin has missed the Penguins' last two regular-season games due to the sinus problem and a knee issue.
"Evgeni Malkin was not out on the ice today and will not be in the game tonight," Penguins Coach Dan Bylsma said after the team's morning skate. "He will also not be going to the all-star game this coming week due to the sinus infection. The symptoms from the sinus infection and pressure in his head are preventing him from going on the ice right now."
Malkin has 15 goals and 22 assists in 42 games this season.