Jan Hejda and Andrew Murray scored in the first period, and Manny Malhotra completed the scoring in the second. Columbus is 1-4-3 against Philadelphia.
The Blue Jackets took advantage of the travel-weary Flyers and an energized sellout crowd of 18,402 - the team's largest of the season - to take the early lead.
Philadelphia was delayed landing in Chicago on Friday and missed the morning skate before losing 5-1 to the Blackhawks on Friday night. Afterward, fog prevented the Flyers' plane from taking off and the team didn't arrive in Columbus until mid-afternoon Saturday.
Hejda scored his second of the season at 3:22. Although the goal was unassisted, Derek Dorsett was instrumental on the play. After coming out of a scramble with the puck to the right of the goal his shot got behind goalie Antero Niittymaki, but Ossi Vaananen was there to clear it off the goal line.
Unfortunately for hVaananen, the puck went straight to Hejda in the left circle and he quickly fired it into the back of the net. It was Columbus' first goal in 131:08.
Columbus has the worst power play in the league, but it converted its second chance at 18:08 for the 2-0 lead. Kris Russell took a pass from former Flyer R.J. Umberger in the left corner and skated around the net before centering to Murray on the opposite side for a one-timer.
Malhotra had the lone goal in the second period. He took a cross-ice feed from Rick Nash and wristed a shot past Niittymaki from the right circle. The score could have been worse heading into the third. Murray hit the right post on a redirect from Umberger in the first and Kristian Huselius clanged one off the crossbar with 52 seconds left in the second.
Niittymaki made 30 saves.
Mason was at his best during a Flyers' power play midway through the second when he stopped Simon Gagne and Scott Hartnell as each was parked in the crease. Mason also made a point-blank pad save of Gagne early in the third.
Notes: Huselius was doubtful after the morning skate because of illness but he was in the lineup and assisted on the third goal. Forward Craig MacDonald was called up from Syracuse of the American Hockey League as insurance, but did not play. ... Philadelphia defenseman Kimmo Timonen suffered a chip fracture of his right ankle Friday and did not play Saturday. He is expected to miss at least a week. ... Hartnell broke a big toe in the Chicago game, but played against the Blue Jackets.