Atlanta (7-1-1) has 15 points, the most ever for the Thrashers in October. Marian Hossa and Steve Rucchin also scored on the power play for the Thrashers, who also got a goal from former Florida captain Scott Mellanby. Vyacheslav Kozlov had four assists.
Atlanta finished 5-for-7 on the power play. The Thrashers entered the game 4-for-31 with the man advantage.
Florida, which entered the game first in the league in power-play efficiency at 27.9, was 0-for-6.
Joel Kwiatkowski, Bryan Allen and Jozef Stumpel scored for Florida, which lost at home for the first time in five games.
Atlanta is 3-0 against Florida this season. The Thrashers beat the Panthers 4-2 at Atlanta on Saturday night.
Kari Lehtonen, who has started every game for Atlanta, made 25 saves.
Florida goalie Alex Auld (3-3-1) gave up five goals on 19 shots before being pulled after the second period with the Panthers trailing 5-2. Ed Belfour stopped seven of eight shots in the third.
Atlanta trailed 2-0 before Kovalchuk scored his first goal at 17:55 of the first period on a one-timer from the slot.
The Thrashers then took advantage of a 5-on-3 to score twice in 36 seconds in the second.
Hossa tied the game 2-2 with his sixth goal in four games when he took a pass across the crease from Mellanby. Kovalchuk then stopped a clearing attempt by Florida in the slot and beat Auld with a wrist shot just under the crossbar.
After Mellanby scored on a breakaway by taking a loose puck coming out of the penalty box, Kovalchuk completed his hat trick when he took a feed from Kozlov inside the blue line, skated in and beat Auld to the glove side.
Florida took a 2-0 lead with two goals in 23 seconds in the first period.
Kwiatkowski, a defenceman moved to forward because of injuries, opened the scoring when he tipped in Steve Montador's slap shot from the point.
Allen then scored on a 3-on-2 rush when he took Olli Jokinen's cross-ice pass and beat Lehtonen on the short side.
Notes: Florida RW Todd Bertuzzi missed his third consecutive game because of back spasms. ... This was Kovalchuk s fifth career hat trick, his first since Jan. 6, 2006 at Pittsburgh. ... Atlanta's previous mark for most points in October was 13, set in 2003 when the Thrashers went 5-3-2-1. ... This was the first game of Atlanta's season-long five-game road trip. The Thrashers play at Carolina Wednesday, followed by games at Philadelphia, Buffalo and Toronto.