Emery notched 13 of his saves in the third period and made a spectacular right-pad save on Sean Monahan with 1:25 remaining after the Flames had cut the Flyers' lead to one.
He racked up his eighth win in 11 career games against Calgary to help the Flyers head into the Winter Olympics break with a fourth straight win.
Brayden Schenn and Claude Giroux scored goals for Philadelphia.
Matt Stajan scored with 2:26 left in the third to make it 2-1, but Calgary could get no closer in falling for the second time in three contests.
Reto Berra turned aside 21-of-23 shots.