Timonen made the go-ahead goal on a shot through traffic from the blue line with 9:32 remaining and added an empty-netter with 41 seconds to play.
James Van Riemsdyk scored the other Flyers' goal, assisted by Timonen.
Philadelphia goalie Brian Boucher made 26 saves.
Vladimir Sobotka scored and Tim Thomas turned in 35 saves for the Bruins.
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