"You can't come in here and think it's going to be an easy two points," Briere said after scoring in his fifth straight game. "It took us a while to get the edge on it."
Philadelphia has won five of six to open a four-point lead over second-place Tampa Bay in the Eastern Conference. The Thrashers have just one regulation win in their last 11 games.
Jody Shelley and Kimmo Timonen gave the Flyers a 2-1 lead, each scoring his second goal during a 21-second stretch late in the second. Jeff Carter added his 18th goal, an empty-netter, in the final minute.
Philadelphia coach Peter Laviolette was pleased to see his team skate hard a night after losing 7-5 at Boston.
"I thought we controlled the game from start to finish," Laviolette said. "But it seemed as they had a few power-play chances, and they made the most of their chances. We found ourselves in a 2-2 game, and their goalie made some big saves. After our game with Boston, I was very happy with how we played."
Before last season, when Atlanta swept Philadelphia in four games by an aggregate 13-6 score, the Flyers won 14 straight in the series.
Giroux, who snapped a nine-game streak without a goal, was certain the Thrashers would put up a fight after a four-day break.
"We knew Atlanta was going to show up, so we got our rest, and I think it paid off in the end," Giroux said. "Any time that you're playing well and the other team is playing well and nothing goes in, it's tough."
Philadelphia scored five goals for the third straight game. The Flyers began the night averaging 3.4 goals per game, second only to Detroit in the NHL.
"It took us a while -- the third period -- to get it going," Briere said. "You try not to get frustrated by [losing to Boston], but the big part of a win like tonight is the confidence it brings."
Briere scored his 24th goal of the season with 7:12 left, beating Ondrej Pavelec with a wrist shot.
"It was 1-0, and they scored to make it 1-1, and we stopped playing," Pavelec said. "Then they scored the second one right away. If they score a goal, we've got to be ready for the next faceoff."
Briere, with six goals and five assists in his last five games, has Philadelphia's longest goal streak since Geoff Sanderson scored in five straight in November 2006.
Briere added to his dominance of Atlanta. In 24 career games against the Thrashers, he has 10 goals and 23 points.
Giroux made it 4-2 with 2:57 left with his 17th goal.
Atlanta defenseman Chris Thorburn hopes his team stays positive despite another setback.
"We are a good team and we know that," Thorburn said. "The effort was there tonight, and it's kind of a letdown when we don't come away with two points, but there were a lot of good things that happened out there. Just a couple of breakdowns."
Philadelphia improved to 30-7-3 against the Thrashers. ... Flyers D Chris Pronger, who has missed the last 11 games to recover from right foot surgery, participated in the morning skate, his first time on the ice with teammates since he was injured Dec. 15. There is no immediate timetable for Pronger's return. ... Ladd has three goals and six points in the last five games. ... Atlanta LW Evander Kane (mid-body) returned from a two-game absence.