Samsonov improved to 9-0-0 at home.
"Last couple games, yeah, I [allowed] eight goals," Samsonov said. "A little bit of a Christmas gift from me, but it's OK, we got the two points today, so that's more important for us. We [will] smile tomorrow with a few days off. I'll just enjoy it and stay with my family and dog."
Tony DeAngelo had a goal and an assist, and Travis Konecny had two assists for the Flyers (11-16-7), who are 2-4-2 in their past eight games. Carter Hart made 30 saves.
"Penalties and just not being able to get pucks behind their defense," Philadelphia coach John Tortorella said. "We fed their transition, we allowed their top guys to get going on the power play. Our second period was atrocious."
Marner put Toronto up 2-1 at 19:23 of the second period when he one-timed a pass from John Tavares in the high slot on the power play.
The Maple Leafs outshot the Flyers 26-8 through the first two periods.
"It's not an easy task for a goalie," Toronto coach Sheldon Keefe said. "I was thinking about it during the game about how we have to do a really good of preventing the big chance because long breaks with no action, and then we saw it in the third period all of a sudden they got two in pretty tight. It's a tough ask for the goaltender there. I feel for them in that sense, yet I don't because our team is playing well in front of them, keeping the chances down, the shots down, so they're going to have to get comfortable in net."
Bunting made it 3-1, extending the lead 33 seconds into the third period when he one-timed a pass from Auston Matthews in the slot.
"That was a great play, that whole sequence I thought we were hard on the forecheck, switching sides and then things opened up," Bunting said. "[Nylander] made a great play to [Matthews] and he could have even shot that, but he saw me and I had an easy tap in so that was a great play by both of them."