With the victory, the Hurricanes extended their division lead to four points over the second-place Washington Capitals and five over the third-place Thrashers.
Eric Perrin, Mark Recchi and Todd White scored for Atlanta.
Thrashers goalie Kari Lehtonen had one of his busiest nights of the season, making 41 saves. Atlanta was hoping for a better showing after being outshot 49-10 by the New York Islanders in a 4-1 loss Sunday.
Even after losing Rod Brind'Amour to a season-ending torn ACL on Feb. 14, the Hurricanes are 4-1-1 in their last six games to carve out a small measure of breathing room in the Southeast.
The Hurricanes peppered Lehtonen with a season-high 21 shots in the first but didn't break through until the middle period.
Eric Staal pressured Lehtonen behind the Thrashers' net, forcing Lehtonen to lose control of the puck. Staal then nudged it to Whitney, who was in front.
The Thrashers scored less than two minutes later when Perrin knocked a rebound of Marian Hossa's shot past Ward.
Carolina went up 2-1 just over a minute later when Bayda redirected shot by Tim Gleason from the point past Lehtonen.
The Hurricanes scored again when Frank Kaberle gathered his own rebound in the slot and slapped it off Samsonov's skate. Samsonov's foot appeared to be off the ground when it redirected the puck in the net, but the play withstood a video review.
Samsonov has scored seven goals in 20 games since Carolina claimed him on re-entry waivers on Jan. 8.
Atlanta trimmed the deficit to a goal late in the period when Ilya Kovalchuk's shot from the point smacked off the end boards and bounced back into the crease. Recchi, who played for Carolina when it won the Stanley Cup in 2006, poked the puck above Ward's glove for a power-play goal. Recchi has scored nine goals in 33 games with Atlanta.
Aucoin and Walker scored early in the third to make it 5-2.
Notes: Atlanta dropped to 12-8-1 against the Southeast Division. ... Staal has seven points in his last five games. ... Four of Atlanta's next five games are on the road. ... The Hurricanes are the only team in the NHL without a defenseman averaging at least 20 minutes of ice time.