Ovechkin stole an apparent victory from Atlanta by scoring the tying goal with only 30 seconds left in regulation. He took the puck from Niclas Havelid following the faceoff to open overtime and scored the unassisted goal. The hat trick gave the Washington star 21 goals for the season.
Jean-Pierre Vigier gave Atlanta a 2-1 lead with less than 6 minutes left in regulation.
The Thrashers suffered their fourth straight loss and fell to 4-1 against Washington this season.
Brent Johnson, starting ahead of Olie Kolzig for the second straight game, made 28 saves for the Capitals.
Jon Sim scored Atlanta's first goal.