Sidney Crosby and Jordan Staal also scored for the Penguins, who beat the Flyers for the third time this season. Malkin one-timed a pass from Mark Recchi in the high left slot and fired a slap shot over Flyers goalie Antero Niittymaki's right shoulder just under the cross bar. Crosby picked up the assist.
Randy Robitaille and Geoff Sanderson had goals for the Flyers, who have lost six in a row and continue to hold the worst record in the Eastern Conference.
Ex-Penguin Robitaille scored the game's first goal, his fourth, 2:14 into the second period. After a Josef Melichar giveaway at centre ice, Robitaille carried the puck in on a 3-on-1. He attempted to get a pass through to a charging Simon Gagne, but the pass was broken up by Pittsburgh defenceman Sergei Gonchar. The puck deflected off of Gonchar's stick and between the legs of goalie Marc-Andre Fleury.
Crosby tied the game with 13:01 to play in the period when he picked up a loose puck just inside the Pittsburgh blue line and took off, ultimately as part of a 2-on-1 with Chris Thorburn. Crosby kept the puck and flipped a wrist shot above Niittymaki's shoulder on the glove side.
Another Philadelphia turnover led to the Penguins' second goal. Former Flyer John LeClair gained possession of the puck near the Philadelphia blue line and got it to Michel Ouellet. Ouellet fed a pass to Staal, who one-timed a slap shot high to Niittymaki's glove side.
It was the sixth goal of the season for Staal, tied for second-most among rookies behind Malkin's nine.
Sanderson tied the game 2-2 when he fired a puck into an open net to the left of Fleury with 13 1/2 minutes to play. A pass from R.J. Umberger bounced off Melichar's stick to Sanderson, who scored for the fourth time this season.
The Penguins had not outshot an opponent during their losing streak, but held a 39-25 advantage in shots Monday and led 31-10 after two periods. The last time the Penguins had more shots than their opposition was during a 4-2 win over New Jersey Oct. 24 - eight games ago.
Notes: Pittsburgh RW Nils Ekman missed the game due to what team officials described as an illness. ... Philadelphia's power play - worst in the NHL on the road at 4.4 per cent coming into the game - was 0 for 5, including a two-man advantage late in the second period. The Flyers' power play ranked tied for 29th overall heading into the contest. ... Pittsburgh had not beaten the Flyers three times in one season since 2000-01. ... Umberger grew up in the Pittsburgh suburb of Plum.