Boone Jenner scored twice, and Eric Robinson had a goal and an assist for the Blue Jackets (5-9-1), who are 2-0-1 in their past three games, including defeating the Flyers for the second time in less than a week (5-2 win on Nov. 10).
Elvis Merzlikins allowed two goals on 17 shots before leaving the game in the second period with an undisclosed injury. He was replaced by Joonas Korpisalo, who made 18 saves.
"You get five of six points here in three games, it's a good stretch with the amount of injuries that have piled up," Columbus coach Brad Larsen said. "We lost ourselves a bit in the second period there, especially the last 10-12 minutes, but we got ourselves together."
Kevin Hayes, Noah Cates and Travis Konecny each had a goal and an assist, and Carter Hart made 28 saves for the Flyers (7-6-3), who have lost four straight (0-3-1).
Philadelphia rallied from two goals down twice to get the overtime point.
"We've been battling back pretty much all year," Hayes said. "You don't want to go down two goals. but's nice to know there's no quit in this room. We all believe together that we can get a goal."
Sean Kuraly gave Columbus a 1-0 lead at 12:36 of the first period when his turnaround shot from the right circle deflected in off the stick of Philadelphia defenseman Justin Braun.
"We score four tonight and we still lose," Flyers coach John Tortorella said. "The first period we didn't play well, but we were better in the second."