Nathan Horton tallied in the second period and Seguin added the final goal for Boston, which snapped the Flyers' seven-game winning streak and notched its 18th victory in 21 contests.
Thomas made 31 saves in the shutout, the 30th of his career.
Philadelphia goalie Ilya Bryzgalov was pulled 7 minutes into the second period after surrendering five goals on 20 shots. Sergei Bobrovsky entered and turned aside 16-of-17 shots the rest of the way.
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