Dan Carcillo and Blair Betts had goals for the Flyers, who are in a three-way tie with Ottawa and Montreal for fifth in the conference with 79 points.
"They played with more passion and desperation than we did," Philadelphia defenseman Chris Pronger said.
Ian Laperriere said the Flyers have to play with the same desperation the Thrashers showed.
"We need these points as much as they do," Laperriere said. "We are not in the playoffs yet."
The Thrashers were in eighth place before losing six straight from March 6-14 to fall to 11th.
"We're fighting for our lives," Atlanta's Eric Boulton said. "We lost all those games in a row, but we're still in it."
Antropov, a 10-year veteran in his first season with the Thrashers, has emerged as Atlanta's scoring leader after the team traded Kovalchuk to New Jersey on Feb. 4 for four players, including Bergfors. Antropov has set a career high with 63 points, including 25 points in his last 21 games.
"That's not important to me," Antropov said of his team points lead. "My goal is for us to get into the playoffs."
Antropov's leadership showed late in the game when he put Philadelphia's Scott Hartnell in a headlock after Hartnell took a swipe at Hedberg. Antropov drew a 2-minute penalty for roughing and Hartnell was called for slashing.
Goals by Bergfors and Armstrong in the first six minutes gave Atlanta a 2-0 lead, and Carcillo answered for the Flyers 8:16 into the first period.
Antropov and Betts traded goals in the second period, leaving the Thrashers with a 3-2 lead.
Little pushed the lead to 4-2 with his follow shot in front of the net midway through the third period. Armstrong added his second goal late in the period.
Philadelphia, which has been good on 23 percent of its power-play chances to rank third in the league, was 0 for 3 with the man advantage.
Boucher, who fell to 5-13-2, is the Flyers' third No. 1 goalie of the season, following injuries which ended the regular seasons of Ray Emery (hip) and Michael Leighton (left ankle sprain). Leighton was injured Tuesday night in a loss at Nashville.
The Thrashers are 3-0 in the season series.
"You can talk the talk, but it comes down to how you walk," Flyers coach Peter Laviolette said. "Tonight they walked with a really good swagger and good pace. We played like it was just another game."
The teams play again Sunday in Philadelphia. Thrashers coach John Anderson said it will be difficult to take two wins in two days over the Flyers.
"I think going into Philly will be a little tougher," Anderson said. "They're going to be a little more prepared. They're going to play hard."
Atlanta's Jim Slater and Philadelphia's Carcillo drew 5-minute penalties for fighting only 39 seconds into the game. About 3 minutes later, Atlanta's Eric Boulton and the Flyers' Ian Laperriere followed them into the penalty box after a fight. ... Slater also drew 2-minute roughing and tripping minors for a total of three penalties. ... The Flyers had only three shots on goal in the second period. ... Atlanta's Chris Chelios was a healthy scratch for the third straight game.
Copyright by STATS LLC and The Associated Press
Arena: Philips Arena Location: Atlanta, Georgia
Referees: Steve Kozari, Chris Lee Linesmen: Jean Morin, Brian Murphy