Travis Konecny and Nolan Patrick each scored a goal and Ivan Provorov had a pair of assists for the Flyers, who won for the first time in three tries against the Bruins this season.
Philadelphia goaltender Petr Mrazek had 36 saves.
Noel Acciari, David Pastrnak and Patrice Bergeron each scored for the Bruins.
Boston goaltender Anton Khudobin stopped 20 of 24 shots.
Patrick scored at 5:31 of the third for a 3-1 Flyers lead, once again regaining a two-goal lead. Jake Voracek and Oskar Lindblom set up Patrick's goal, his 11th in the last 14 games.
The Flyers couldn't hold the lead as the Bruins quickly got within 3-2 with 13:06 left as Pastrnak's shot deflected off Andrew MacDonald and into the net.
Boston went with an extra skater for the final 1:36 when it pulled Khudobin. The move paid off as Philadelphia wasn't able to clear the puck and the Bruins tied the game at 3 with 3.8 seconds left as Bergeron scored to send the game into overtime.
The Flyers took a 2-0 advantage just 25 seconds into the second when Konecny moved the puck through two Bruins and scored a spectacular goal. Konecny has been red hot lately and recorded his 24th goal of the season.
Philadelphia had a two-on-none break and couldn't score and the Bruins came right back and sliced the lead in half to get within 2-1 when Acciari scored with 5:35 remaining.
The Bruins led 29-15 in shots on goal through two periods.
Giroux gave the Flyers a 1-0 lead with 10:22 remaining in the first with an impressive one-timer into the back of the net. It was Giroux's 28th goal of the season, tying a career high before setting a new mark in overtime. The captain also scored 28 goals in the 2011-12 and 2013-14 seasons.
The Bruins had more scoring chances in the first, outshooting the Flyers 12-7. But Giroux put the Flyers ahead and Mrazek stopped all 12 Boston shots.
--Field Level Media
Boston | Philadelphia | |
David Backes 2 | Points | Claude Giroux 2 |
Noel Acciari 1 | Goals | Claude Giroux 2 |
David Backes 2 | Assists | Ivan Provorov 2 |
David Pastrnak 1 | Power Play Goals | N/A |
N/A | Short Handed Goals | N/A |
Anton Khudobin .833 | Save Percentage | Petr Mrazek .923 |
Anton Khudobin 20 | Saves | Petr Mrazek 36 |
Team | Shots | Goals | Power Play | Penalty Kill | Penalty Mins | Face Offs Won |
Boston | 39 | 3 | 1-3 | 2-2 | 4 | 27 |
Philadelphia | 24 | 4 | 0-2 | 2-3 | 6 | 24 |