Marc-Andre Fleury stopped 32 shots for the Penguins, who won their sixth straight home game.
Malkin missed two games last week after being injured during a morning skate. He looked fine while bulling his way toward the net 4:16 into the second period for his eighth goal of the season. Crosby pushed his season-point total to an NHL-best 43 when he deflected in a shot by Pascal Dupuis midway through the third.
Matt Calvert scored with less than a minute left for Columbus, spoiling Fleury's shutout bid. Curtis McElhinney made 28 saves but the Blue Jackets struggled again in Pittsburgh.