After the Bruins spotted the Devils a 1-0 lead, Shawn Thornton rallied Boston with a first-period goal and Chara's second-period power-play goal put the Bruins ahead to stay.
Thomas broke a four-game losing streak for Boston, which maintained a slim lead over Montreal in the Northeast Division with second win in eight games.
Ilya Kovalchuk found the net and Martin Brodeur made 26 saves for the Devils.
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