Dion Phaneuf, Clarke MacArthur and James van Riemsdyk, against his former team, also scored for Toronto, which got its second victory in six games at home this season.
But the win came at a cost. James Reimer stopped 12 shots before being replaced by Ben Scrivens early in the second period with what appeared to be a left leg injury.
Reimer stayed down before being helped to the locker room without putting any weight on his left leg. The Leafs described the injury as a "lower-body injury."
Scrivens finished with 32 saves.
Wayne Simmonds and Tye McGinn scored for Philadelphia. Ilya Bryzgalov made 10 saves on 14 shots before being replaced by Brian Boucher after MacArthur's goal at 6:15 of the second. Boucher finished with nine stops the rest of the way.
Tied 1-1 after the first, the Leafs took control early in the second.
The bruising Orr, who has been rejuvenated this season under coach Randy Carlyle, scored his goal of the season at 2:05. Frattin then added his seventh of the season in just 10 games since being called up from the AHL. He deflected a Cody Franson shot home just 28 seconds later. Franson had assists on both goals.
The Leafs didn't miss a beat after Scrivens replaced Reimer a short time later as Nazem Kadri, who also finished with two assists, found MacArthur in front on a slick pass to end Bryzgalov's night.
The Flyers had a chance to get back in it when Toronto defenseman Korbinian Holzer was assessed a five-minute penalty for boarding and a game misconduct at 13:31 for a hit on McGinn.
But Scrivens held off the Flyers, including a big glove save on Brayden Schenn in tight.
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Van Riemsdyk put the game out of reach with his team-leading eighth of the season on a shot that squeaked past Boucher just 71 seconds into the third.
McGinn scored with 32 seconds left in regulation for Philadelphia.
Coming off a 3-0-0 road trip, which included a resounding 6-0 victory in Montreal on Saturday night, the Leafs came out slow Monday.
Philadelphia worked the puck into the Toronto end and kept it there until Simmonds banged the rebound of a Luke Schenn shot home just 38 seconds in.
Schenn played 310 games in four seasons with the Leafs before being traded to Philadelphia in June for van Riemsdyk. The deal was viewed as a fresh start for both former top-five draft picks and reunited Schenn with his brother, Brayden.
Philadelphia carried the play against the Leafs for much of the rest of the first period until Mikhail Grabovski, who was cleared earlier in the day of any wrongdoing in an alleged biting incident against Montreal on Saturday, hit both posts behind Bryzgalov only to see the puck stay out.
That chance seemed to spark the Leafs and Phaneuf tied the game at 14:49 with a one-timer off a pass from Leo Komarov that beat a screened Bryzgalov.
NOTES: The Leafs are 6-1-0 on the road this season. ... Luke Schenn, who wears No. 22 with Philadelphia, started for the Flyers on defense and got a small applause from the crowd about 10 minutes before the opening faceoff. The Leafs honored Schenn midway through the first period for his work supporting the Canadian military. ... Philadelphia was coming of a 3-0-1 homestand. Monday's game was the first of a six-game road trip that will also see the Flyers travel to Winnipeg, New Jersey, Montreal, Long Island and Pittsburgh. Philadelphia is 1-6-0 away from home.
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