But Seguin responded by sliding a shot past a sprawling Ilya Bryzgalov and Thomas made it hold up with a blocker save on Wayne Simmonds on Philadelphia's last chance.
Seguin, Krejci, Patrice Bergeron and Milan Lucic each notched a goal and an assist in regulation and Thomas made 33 saves as the Bruins improved to 9-0-1 in their last 10 regular season games at Philadelphia and grabbed a share of the Eastern Conference lead.
Hartnett logged a natural trick the second period, scoring his 23rd, 24th and 25th goals in succession, and Max Talbot scored twice for the short-handed Flyers, who were without high-scoring Jaromir Jagr and Danny Briere.
Bryzgalov made 32 stops in the loss.
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