Jones' shot with two minutes left in overtime caromed into the net off Boston defenseman Andrew Ference to lift the Flyers to a 4-3 win over the Boston on Saturday.
There was spattering of boos nearly every time Jones touched the puck. Last season, he hit Patrice Bergeron into the boards from behind, giving him a concussion and broken nose. Bergeron, one of the Bruins' best young players, missed the remainder of the season from the aftereffects of the hit on Oct. 27.
On Saturday, the Flyers defenseman knew what he'd be going through in his second trip to Boston since the incident.
"It doesn't bother me if they want to boo me or cheer me or say whatever to me, it's another game," Jones said. "It was important game for us. The way we bounced back in the second was a big step for us."
Former Bruin Glen Metropolit, Scott Hartnell and Simon Gagne also scored for the Flyers, who overcame a 3-1 deficit, and won for the second time in five games.
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.
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"It's just one of those you have when the puck goes in the net," Ference said. "I saw it. I really didn't have time to react. It's always nice when you score those."
The Flyers pulled goaltender Martin Biron after the first period. Backup Antero Niittymaki stopped all 22 shots he faced.
Philadelphia played its NHL-high 18th overtime. The Flyers entered the day sixth overall in a tight Eastern Conference race for eight playoffs spots.
"Nitty came in and made some big stops for us. We got two points," Hartnell said. "We're not looking to catch Boston, we're looking to get in the playoffs."
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 tabbed for the right corner with 4.5 seconds left in regulation temporarily saved the game for Boston.
Fernandez, sidelined with a sore back since early January, made 26 saves.
"We didn't give him much help," Boston coach Claude Julien said. "He hadn't played in over a month so we couldn't necessarily expect him to stand on his head and bail us out."
Fernandez elected not to talk to the media.
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.
Philadelphia was 0-for-13 on the power play in its previous two games.