It was the Flyers' eighth straight win over the Thrashers. The Flyers are 12-2-1 all-time at Atlanta and overall have won 23 of 30 games in the series, including two games this season.
The Thrashers led 1-0 before the Flyers scored four second-period goals.
Carter scored at the end of a power play to give Philadelphia a 2-1 lead 13:42 into the period. Then, at the 13:55 mark, Carter scored again on a wrister from the top of the right circle.
Carter, who had a goal and an assist in a 4-0 win over the Thrashers on Oct. 16 in Philadelphia, has seven goals and four assists in 10 career games against Atlanta.
Scott Hartnell added the 100th goal of his career with one second left in the period for a 4-1 lead. Hartnell's short-handed goal came off a pass from James Dowd.
Hartnell had two assists, including one to set up the Flyers' first goal, by Steve Downie, only 32 seconds into the second period.
The Flyers are 4-1 on their six-game road trip which ends Thursday against the New York Rangers.
Ilya Kovalchuk's league-leading 35th goal midway through the opening period gave the Thrashers a 1-0 lead.
Antero Niittymaki shut out the Thrashers the rest of the way, stopping 27 shots to win the battle of backup goalies.
Atlanta's Johan Hedberg started his second straight home game ahead of Kari Lehtonen after making a season-high 37 saves in a 5-2 win over Buffalo on Sunday. Hedberg made 25 stops but couldn't overcome the Flyers' second-period scoring outburst.
Niittymaki started ahead of Flyers regular Martin Biron, who shut out Atlanta 4-0 on Oct. 16 at Philadelphia. Niittymaki stopped 54 of 56 shots in a 3-2 win at Toronto on Saturday, but his 6-0-0 career record and 1.68 goals against average against Atlanta may have played the larger role in his start.
Atlanta's Chris Thorburn and Philadelphia's Riley Cote traded punches with less than 5 minutes left. Each drew 5-minute penalties for fighting, and Thorburn also drew an interference penalty.
Notes:
Flyers F Sami Kapanen was held out after needing about 25
stitches to close cuts on his face after Saturday's game at
Toronto. He also needed dental work after he was hit in the face by
a deflected puck. ... Carter's only other two-goal game of the
season was Dec. 22 against Buffalo. ... Atlanta's last win over the
Flyers was on Nov. 18, 2005 in Philadelphia.
