Ilya Kovalchuk scored the game's lone goal in the first period after an assist by Scott Mellanby, as the Thrashers won for the second time in their last three games.
Alex Auld stopped 27 of 28 shots for the Panthers, who have lost three games in a row and four of their last five.
On the power play, Florida was 0-for-7, and Atlanta was 0-for-3.
The Thrashers have won all four games against the Panthers this season. In those four games, Atlanta has out-scored Florida, 17-5.
Saturday's win gave Coach Bob Hartley his 300th career victory.