The Penguins led 2-0 after the first period and made the contest a laugher by increasing their lead to 5-1 heading into the third.
Malkin's goals in the first and second periods gave him 40 this season and Sykora's total rose to 24.
They played their seventh straight game without high-scoring center Sydney Crosby (high ankle sprain).
Philadelphia's lone goal was the Mike Knuble's 27th at 12:43 of the second.
The Flyers have lost their last four games.