The previously unbeaten Sabres lost for the first time in the new NHL season.
Regulation ended in a 2-2 tie when Buffalo right wing Jason Pominville scored unassisted at 16:52 of the third period.
Thomas Vanek scored Buffalo's other goal on the power play at 17:00 of the second.
Netminder Patrick Lalime gave up two goals on 37 shots for the Sabres, who were off to a 4
Buffalo went 1-for 5 on the power play, and the Thrashers failed to score after six man-advantage chances.
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