The victory, combined with the Pittsburgh Penguins' 6-2 loss to the Colorado Avalanche, pushed the Blue Jackets into second place in the Metropolitan Division. The Blue Jackets hold a one-point lead over the Penguins.
Mathieu Olivier also scored, Damon Severson had two assists, and Jet Greaves made 24 saves for Columbus (38-22-11), which won for the ninth time in 14 games (9-1-4).
Sean Couturier and Jamie Drysdale each scored, and Dan Vladar made 16 saves for Philadelphia (34-24-12), which had its three-game winning streak and six-game point streak (5-0-1) ended.
The Flyers are five points out of the second wild-card spot with 80 points.
Couturier, who had missed Philadelphia's past two games with an upper-body injury, gave the Flyers a 1-0 lead at 17:07 of the first period. Rasmus Ristolainen's shot into traffic was knocked down in the crease by Luke Glendening. He slid the puck across the crease to Couturier, who tapped it in at the left post.
That came after Philadelphia forward Noah Cates was stopped on a penalty shot at 13:28 that was prompted by a hook on Cates' break out by Columbus forward Kirill Marchenko.
Olivier tied the game 1-1, 44 seconds into the second period. Werenski skated the puck through the middle of the Philadelphia zone, drawing two defenders toward him. He found an open Olivier in the right face-off circle, and the forward scored past Vladar's glove.
Werenski put the Blue Jackets ahead 2-1 at 2:28 when he beat Vladar under his glove with a wrist shot from the hash marks.
Marchment made it 3-1 at 4:38 of the third period when his one-timer from the left face-off dot beat Vladar over his right shoulder. Play continued, however, and the goal was called after a video review showed the puck crossed the goal line in a legal fashion.
With Vladar pulled for the extra attacker, Drysdale's blast from the point cut it to 3-2 at 17:56.
