Stuart began the scoring with his second goal this season at 3:31 of the first. His second goal of the game, at 9:57 of the third, capped Boston's scoring.
Atlanta was led by Todd White's goal and assist. Boris Valabik (unassisted) and Slava Kozlov (power play) also scored once each.
Goaltenders Johan Hedberg and Ondrej Pavelec were beaten seven times on just 25 shots for the Thrashers, who have dropped seven of eight.
On the power play, Boston went 2-for-3, and Atlanta went 2-for-4.