Glen Murray scored his 20th goal of the season for Boston, his fifth straight season with 20 or more. Patrice Bergeron had the other goal for the Bruins, who lost their last three games by a combined score of 20-3.
Sami Kapanen scored twice for Philadelphia, which had won three of its last four games.
Mike Knuble scored for the Flyers with 1:55 to play after they pulled their goaltender, but the Bruins had trouble getting the puck past centre ice the rest of the game.
Bruins defenceman Zdeno Chara missed a game for the first time this season with a lower body injury.
Tim Thomas made 29 saves for Boston.