Ron Hainsey scored 1:17 into overtime for the Thrashers, who rallied from a three-goal deficit and stormed back for a 5-4 victory on Saturday night.
Even a hat trick by Philadelphia's Ville Leino couldn't derail the Thrashers, who are still a long shot to make the playoffs but now have some momentum on which to build.
The last time Philadelphia blew a three-goal lead after two periods and lost was Nov. 21, 1987, when the Flyers were beaten 6-4 by the New York Islanders after leading 4-1.
Andrew Ladd tied it 4-4 with 45 seconds left in regulation to set up Hainsey's heroics.
In overtime, Evander Kane carried the puck down the right side, controlled it around sliding defenseman Kimmo Timonen, and centered a pass to Hainsey, whose shot caught a piece of goalie Sergei Bobrovsky and went in.
"This is a game that you don't forget easily," coach Craig Ramsay said. "We've had some games this season where we played so well and so hard. This game we were rewarded. I'm looking at the shot totals and going, 'Oh my gosh, we're going to hit 40 again and have it not work.' Every single player put their heart and soul into the game."
Hainsey's shot was Atlanta's 41st.
Philadelphia built its lead with a pair of goals from Leino and a short-handed tally from Timonen to chase Atlanta goalie Ondrej Pavelec.
Something had to change.
"We just looked at it as a group, and I said, 'What else can I add?'" Ramsay said. "I didn't know what to say. They've done everything I asked and it hadn't worked. So I passed the honors to [goaltending consultant] Clint [Malarchuk] and he said, 'We should change the goalie, shake things up a little bit.'
"We went out and we played. They dug down."
Kane began the comeback with an unassisted goal at 1:09 into the third, scooping up a loose puck, then holding off defenseman Sean O'Donnell and driving down the right side to beat the rookie goalie for his 18th goal and first in nine games.
Bogosian got Atlanta within 3-2 at 12:15.
Leino restored the Flyers' two-goal lead just 1:17 later during a power play. The goal, set up after Atlanta's Mark Stuart was called for playing with a broken stick, was scored with a one-timer past Chris Mason's stick side.
The Thrashers kept fighting and got even with a pair of goals in the final three minutes of regulation. Bogosian scored first, then Tobias Enstrom.
Philadelphia has lost five of eight and is struggling to stay atop the East. They lost for only the second time this season when leading after two periods.
"It's been like this the last few games," Timonen said. "We stop playing. When you stop playing in this league you are going to lose games. This game is about hard work and making simple plays. It seems like every time we get it to be 3-0, 4-0, or whatever, we start turning the puck over. We think the game is over. It's not. That's one of those things we have to change now."
Leino gave the Flyers a 1-0 lead 14:11 in on a well-designed play. Danny Briere delivered the puck from behind the net to Scott Hartnell, who fed Leino on the right side. Leino knocked down the puck with his right skate and fired a wrist shot past Pavelec, who played the first two periods before being replaced by Mason.
Timonen scored a short-handed goal -- Philadelphia's NHL-leading 12th this season -- in the second period. Flyers captain Mike Richards faked a shot, then sent a pass to a waiting Timonen, who easily slapped a shot into the open net.
Leino scored his second nearly 10 minutes later, diving for a rebound of Richards' shot. Richards finished with three assists.
Hainsey made all of that irrelevant. The Thrashers still have hope as they get ready for their final 13 games, eight of which will be played on the road.
"We have to win," Hainsey said. "The position we're in, we have to win a large majority, probably .800 hockey. If we get a stretch where we don't get wins in two or three in a row, that'll probably be the end of us. As long as we keep winning, we'll be in the conversation."
Philadelphia D Chris Pronger missed his second straight game with a right wrist injury. The Flyers hope to have him in the lineup Tuesday at Florida. ... Atlanta forward Patrice Cormier is out indefinitely with an undisclosed upper body injury. ... The Flyers are 31-7-3 against the Thrashers, who went 4-0 last season against Philadelphia. ... Leino's hat trick was the second by a Flyers player this season. Carter did it on Nov. 11 at Carolina.