Sean Couturier,
Phil Varone
and James van Riemsdyk scored for Philadelphia (14-16-4), which had won two in a row. Rookie goalie Carter Hart made 15 saves and lost for the first time in three games since being called up from Lehigh Valley of the American Hockey League on Monday.
It's the first loss for the Flyers since coach Scott Gordon was promoted from Lehigh Valley after Dave Hakstol was fired Monday.
"I think we did a good job. We carried the play a lot," van Riemsdyk said. "Obviously we made a couple mistakes that ended up in our net, but those are things we can clean up. But I think overall we had a pretty good process, we played pretty hard and did a lot of good things."
The Blue Jackets had a season-low 19 shots on goal.
"We did not play that well tonight," Tortorella said. "We played in spurts. It was probably [Bobrovsky's] best game of the year. ... We weren't awful, but we didn't play with pace and we had some passengers tonight."
Werenski gave the Blue Jackets a 1-0 lead at 15:05 of the first period with a shot from above the hash marks.
Couturier made it 1-1 when he scored a power-play goal for Philadelphia with 23 seconds left in the first, and Varone gave the Flyers a 2-1 lead at 7:40 of the second period with his first NHL goal since Jan. 16, 2016.
But Atkinson scored on his rebound at 9:30 to tie it 2-2, then gave the Blue Jackets a 3-2 lead at 13:23.
Atkinson has 22 goals in 34 games, two shy of the 24 he scored in 65 games last season. He's on pace for 51 this season; his NHL high is 35 in 2016-17.
"I like scoring goals," he said. "I don't care how many I get as long as I'm scoring goals. Just a lot. And more."
Panarin scored for Columbus with 36 seconds left in the second to make it 4-2. He one-timed a shot past Hart after Dubois beat Couturier on a face-off in the right circle in the Philadelphia zone.