Chris Kelly and Tyler Seguin scored for Boston, and Thomas made 27 saves in regulation and the five-minute overtime. Thomas, the reigning Vezina Trophy winner, is 6-0 in shootouts this season.
Ilya Bryzgalov made 31 saves for the Flyers, who lost for just the second time in nine games. Matt Read and Jakub Voracek scored for Philadelphia.
The Bruins passed Ottawa and took over first place in the Northeast Division and the No. 2 seed in the Eastern Conference heading into the Senators' game against Toronto on Saturday night.
David Krejci and Seguin scored for Boston to open the shootout, answered by Read and Claude Giroux. Patrice Bergeron beat Bryzgalov on the stick side, leaving Briere with a chance to tie it.
The Flyers center skated in quickly on Thomas but found himself too close to the crease. Pulling up, he put a weak shot right into Thomas to end it.
The Bruins had allowed 21 goals over the last four games, losing all of them. Bryzgalov had won seven in a row, posting a 0.99 goals-against average.
The Bruins had given up the first goal in seven straight games. But they took the lead 6:23 into the first period when Kelly knocked in a rebound of Benoit Pouliot's shot. They made it 2-0 when Patrice Bergeron made a pass from behind the net to Seguin on the side of the crease and he put it in with 2:53 left in the first.
