Byron Bitz scored his first NHL goal for Boston, and Marc Savard and Chuck Kobasew had the other two.
About 55 seconds after Boston's Dennis Wideman's redirected shot hit the right post, Jones fired a seemingly harmless shot that was clearly wide of the net, but the puck hit Ference's body and caromed into the net.
The Flyers pulled goaltender Martin Biron after the first period. Backup Antero Niittymaki stopped all 22 shots he faced.
There was spattering of boos nearly every time Jones touched the puck. He had checked Boston's Patrice Bergeron into the glass last season and Bergeron missed most of the season with a concussion and the aftereffects from the hit.
Bitz and Kobasew scored 8 seconds apart late in the first period, giving the Bruins a 3-1 edge. It matched the fastest consecutive goals for Boston since Barry Pederson and Norman Leveille did it Dec. 20, 1981.
Bitz knocked a rebound of Mark Stuart's blueline shot behind Biron, and Kobasew skated down the right wing from the face off and slipped a wrister between his pads.
But the Flyers tied it when Metropolit and Scott Hartnell scored 4:17 apart in the second. Hartnell's tally came on the power play when he beat Manny Fernandez with a backhander from the edge of the crease.
Fernandez's glove save on Jeff Carter's uncontested shot labeled for the right corner with 4.5 seconds left in regulation temporarily saved the game for Boston.
Philadelphia was 0-for-13 on the power play in its previous two games.
Fernandez, sidelined with a sore back since early January, made 26 saves.
Boston had taken a 1-0 lead on Savard's goal off a weird angle 3:52 into the first. He collected a rebound behind the net, circled in front and fired a shot that slipped behind Biron.
Skating with a two-man power play, Philadelphia tied it 1-all when Gagne scored from the edge of the crease at 14:57.
Notes: The NHL-leading Bruins face the Western Conference-leading San Jose in their next game at the TD Banknorth Garden on Tuesday. ... Boston center Michael Ryder missed the game and is out "indefinitely" with a fractured facial bone. Coach Claude Julien said before the game that he would undergo more tests Monday. ... The Bruins are 7-0-4 against Atlantic Division teams this season. ... Bruins D Aaron Ward was out with the flu - as were Philadelphia's RW Scottie Upshall and C Mike Richards, who both missed the last game. ... Boston beat the Flyers 3-1 in Philadelphia on Wednesday.
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