Atlanta ended a season-high nine-game winless stretch Sunday but trailed 1-0 midway through the second period in this one. Kovalchuk set up a power-play tally by Vyacheslav Kozlov with 6:29 left in the period, sparking the Thrashers to their second win in as many meetings with Buffalo this season.
Kozlov also scored late in the third period for Atlanta, which has outscored the Sabres, 11-5, in 2003-04. Patrik Stefan and J.P. Vigier had the other goals for the Thrashers.
Nurminen kept Atlanta in the game early, turning aside 18 of 19 shots over the first two periods.
J.P. Dumont scored the lone goal for Buffalo, which fell to 2-11-1 in its last 14 road games.