Cam Ward stopped 31 shots for the Hurricanes, who were off to an 0-3-1 start.
An overtime period seemed inevitable until Whitney's first goal of the season in the final second. Whitney tipped in a shot by Eric Staal.
The last-second shot capped a frustrating night for Atlanta goaltender Kari Lehtonen, who gave up three first-period goals and then shut out the Hurricanes until Whitney's game-winner.
Craig Adams scored two goals for Carolina.
Jon Sim scored two goals in a 22-second span in the second period for Atlanta, which opened the season 3-0-1.
Carolina gave up 18 goals in the first four games, second-most in the league, and was outscored 11-5 in the first two games of its seven-game road trip. Carolina coach Peter Laviolette challenged his team to end the malaise, and the Hurricanes answered early against the Thrashers.
Lehtonen, who allowed only three goals in the first four games, had that total doubled in the Hurricanes' strong opening period.
Adams scored on two tip-ins for Carolina's first two goals. On each score, Lehtonen stopped shots - by Erik Cole on the first and Niclas Wallin on the second - but Adams was in position to put in the deflections.
Carolina took a 3-0 lead with less than two seconds left in the first period when Staal scored on a breakaway. The goal came after Atlanta's Ilya Kovalchuk was denied on a breakaway by Ward, and the Hurricanes quickly moved the puck back down the ice for Staal's wrist shot.
Officials needed a review to confirm Sim's first goal with less than six minutes left in the second period. Capping a furious battle for possession of the puck in front of Ward, Sim managed to tip in a shot by Glen Metropolit.
Only 22 seconds later, Sim scored again, cutting the Carolina lead to 3-2.
That lead held until Bobby Holik's game-tying goal with less than six minutes left in the third period.
Carolina was 0-for-5 on the power play and Atlanta was 0-for-4.
Notes: Carolina captain Rod Brind'Amour earned his first two points of the season with assists on Adams' goals. ... Kovalchuk, who since the start of the 2002-03 season leads all players with 131 goals, still does not have one this season. He was stopped on 10 shots. ... Sim, who had 17 goals for Philadelphia and Florida last season, already has four this season. ... Lehtonen is 1-4 in five career starts against Carolina.