Michael Ryder also scored for the Bruins, who improved to 38-8-6.
Scott Hartnell had the lone goal for the flu-ridden Flyers. Philadelphia captain Mike Richards, defenseman Braydon Coburn and forward Scottie Upshall each sat out due to the virus.
The Flyers have lost five of eight games to drop to sixth in the Eastern Conference after a brief stay atop the Atlantic Division.
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