Gagne, the longest-tenured Flyer, played for the first time since he broke his right toe in Game 4 of Philadelphia's opening-round series against New Jersey.
Game 5 is Monday at Boston. The Bruins can still advance to their first conference finals since 1992 with a win on their home ice.
Former Flyers star Mark Recchi scored twice for the Bruins - including the tying goal with 31.5 seconds left in regulation that made it 4-all.
Chris Pronger, Danny Briere, Claude Giroux and Ville Leino all scored for the Flyers.
Michael Ryder and Milan Lucic had Boston's other goals.
Gagne was expected to at least miss this round after being injured while blocking a shot. He was walking around the Flyers' practice facility this week and was hopeful he could start skating this weekend.
He managed an early comeback and heard a rousing ovation when he was introduced in pregame introductions. Gagne got the crowd roaring 3½ hours later on his first goal of the postseason.
The Flyers wasted a 3-1 lead and were deflated when Recchi scored the tying goal.
Recchi burned his former team when he scored against Brian Boucher off a faceoff in Philadelphia's end. The sounds of "Booooosh" that echoed after every late save turned to "booooo" after the Flyers were headed to OT. It was Recchi's sixth goal of the postseason.
The Flyers appeared to have forced Game 5 minutes earlier in the third. Leino skated across the slot and tipped in Pronger's shot with 5:40 left for a 4-3 lead that sent the crowd into a frenzy.
As they have in all but one game, the Bruins scored first.
Recchi found the net high off a rebound over a sprawled Boucher to give Boston yet another early boost.
It looked as though that goal would be enough to give the Bruins the lead heading into the second period, but Briere scored on a slapper from the circle that went through Tuukka Rask's to tie it. Gagne's return paid earlier dividends when he won a faceoff early in the second. The puck found its way to Pronger, who scored his fourth goal of the playoffs on a blast from the point that made it 2-1.
The Flyers took their first two-goal lead of the series 4 minutes later on an opportune kick. Scott Hartnell kicked the puck in the crease to a crashing Giroux.
That still wasn't enough to put away the Bruins.
The strangest goal of the game - maybe the series - came midway through the second period. Ryder snapped his stick on a shot that went wide of the net, bounced off the boards and somehow found its way past Boucher. Boucher dropped to his knees for the quick cover, but he either let it knock off his skate, or his pad was punched by Boston's Vladimir Sobotka to allow the puck scooted by.
Either way, the Bruins were suddenly back in the game.
The Bruins erased the deficit in the third when Lucic redirected the puck for a power-play goal that made tied it 3-all and silenced the crowd.
NOTES: Former Flyers stars Keith Primeau and John LeClair were at the game and got huge ovations. ... The Flyers improved to 25-33 in the playoffs when facing elimination.
