Auston Matthews, Calle Jarnkrok, Conor Timmins, Zach Aston-Reese and Timothy Liljegren also scored for Toronto, which swept its three-game season series with the Flyers.
Marner, selected Thursday to the NHL All-Star Game, upped his team-leading points total to 49. Matthews trails Marner by two points after getting his 20th goal. Matt Murray made 34 saves.
''We made good on a lot of our chances and obviously scored a bunch of goals and that put us in a good spot in the game,'' Maple Leafs coach Sheldon Keefe said. ''I didn't think we had our best game by any means, relied on our goaltender probably too much, but he was terrific.''
Nick Deslauriers and Travis Konecny scored for the Flyers, who entered on a season-high four-game winning streak. Carter Hart had 29 saves.
''We self-destructed,'' Flyers coach John Tortorella said. ''We can't overcome some of the things we give them for free.''
Tortorella benched defenseman Tony DeAngelo after just one shift in the second period. DeAngelo, who is third on the Flyers in points with 23, committed a turnover when he misplayed the puck deep in Philadelphia's zone on Aston-Reese's first-period tally that made it 2-0.
''I'm not going to discuss it here,'' Tortorella said tersely when asked why he sat DeAngelo.
''I'm not going to talk if it's justified or not,'' DeAngelo said. ''I didn't have a good first period or start to the second period. It won't be the last time I have a bad game or get sat. I'm not going to go crazy into it. No player ever agrees with getting sat, but we aren't here to question the coach.''
Toronto took control with three goals in a dominating second period.
Timmins opened the scoring 7:01 into the period with his first career goal on a wrist shot from above the right circle to make it 3-1. After Deslauriers beat Murray with a backhander from close range 1:49 later to pull Philadelphia to 3-2, Liljegren recorded a short-handed tally on a slap shot off a faceoff draw to make it 4-2.
Tavares then capitalized on a turnover by Morgan Frost and scored on a wrist shot over Hart's right shoulder that put the Maple Leafs up three goals with 7:38 left in the period.
The Leafs improved to 11-6-3 on the road while upping their scoring margin to plus-33, having scored 141 and allowed 108.
Konecny extended his goal streak to a career-best six consecutive contests when he tallied on a wrist shot that went between Murray's legs with two minutes left in the first, pulling the Flyers to 2-1. It also gave Konecny points in eight consecutive games. He has nine goals and six assists over that stretch.
NOTES: Philadelphia wore Ed Snider Youth Hockey Foundation jerseys during warmups in honor of their late founder and former owner, who would have turned 90 on Friday. Snider passed away in 2016. . Philadelphia fell to 8-10-1 at home. . Jarnkrok had two assists. . Marner has 34 assists on the season.
Maple Leafs: Host Nashville on Wednesday night.
Flyers: At Buffalo on Monday night.
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