It was Washington's sixth straight victory and kept the Capitals seven points in front in the Northeast Division.
Ovechkin, who has scored twice in four of the last six games, raised his season goal total to 13. After leading the league in goals each of the last two seasons, Ovechkin began the night on top of the list again.
Washington took a 3-0 lead into the third period, but Atlanta closed within one on scores by Zach Bogosian and Todd White -- the second of those coming with 2:23 to play.
Mike Knuble clinched it by scoring into an empty net with 53 seconds remaining, which proved to be a necessary goal when Bogosian tallied again on a slap shot with less than a second left.
Semyon Varlamov improved to 4-0 this season by making 39 saves. Ondrej Pavelec stopped 28-of-31 shots for the Thrashers, who have lost four straight.
Copyright 2009 by United Press International.