Steve Eminger opened the scoring 2:48 into the opening period and the Lightning built a 4-0 lead on St. Louis's goals and one by Ryan Malone before Atlanta scored with just 22 seconds left in the game.
Mike Smith made 27 saves for Tampa Bay, which ended a three-game losing streak.
Erik Christensen scored for the Thrashers, who have lost five of their last six contests.
Atlanta goaltender Kari Lehtonen was credited with 31 saves.
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