"We knew it was going to be a tough game, and the boys deserve a lot of credit," Atlanta coach Bob Hartley said. "There was no room out there. You had to fight for every inch of ice."
Carolina had won its previous 21 games when it led going into the final period.
"It was a big game," Carolina coach Peter Laviolette said. "We're playing for our division and a stake in the post season. The whole game is frustrating."
The Thrashers, who kept pace with Tampa Bay for the Southeast Division lead, snapped a four-game losing streak and kept Carolina from climbing further up the Southeast standings. The Hurricanes had won five of their last seven.
"It's huge to get a win like this," Hossa said. "It was a divisional game and it was a big confidence booster for us."
Kovalchuk got the go-ahead goal with a rising slapshot from just inside the Carolina blue line with 2:24 left in the game. Boulton added the insurance goal with just over a minute left in regulation when he put away a second rebound.
Rod Brind'Amour had given the Hurricanes a 1-0 lead with 2:34 left in the second period but it wasn't enough. His goal was set up by Ray Whitney, who skated the puck up the ice and made a spinning pass to Brind'Amour as he charged up the left side.
Brind'Amour flicked a shot that Hedberg wasn't able to stop. It was his 19th goal.
Hossa tied the score at 1-1 at 5:53 for Atlanta when he scored the Thashers' seventh short-handed goal.
His goal started with an innocuous pass from goalie Johan Hedberg, who cleared the puck the length of the ice. Hossa beat Carolina's defense to the puck in the corner and slapped a hard shot along the goal line where it bounce in between Cam Ward's skate and the post.
"I got there first and I saw the goalie and I just shot it at his foot pretty hard," Hossa said. "First, I thought I had it, then I saw the puck slowly getting in. It kind of surprised me."
It surprised Ward, too.
"Anytime you give up a goal like that you try to forget about it as quickly as you can. All I can do is try to forget about it and move on," Ward said.
Hedberg (6-4-1) stopped 33 of 34 Carolina shots to earn his first win since Dec. 5 at Toronto. Hedberg got the start over Kari Lehtonen, who had given up four goals in each of his last two starts and had lost three straight. Ward (25-26-6), playing in his eighth straight game, made 20 saves.
Carolina LW Erik Cole was scratched just before the start of the game with a lower body injury. ... Carolina D Niclas Wallin turned 32. ... Kovalchuk got his 33rd goal, while Hossa recorded his 34th.