Jean-Sebastien Giguere turned away a shot by Matt Read in the shootout and had 31 saves for the Avalanche, who are 8-1 after regulation and undefeated in six shutouts.
The Flyers tied it in the final minute of regulation with their goalie pulled, on Wayne Simmonds' 10th goal of the season. He punched the puck in from up close amid heavy traffic in front of the net.
The Avalanche took a 2-1 lead with the help of a deflection, two actually. Rookie Brad Malone's pass in the offensive zone glanced off the skate of Philadelphia's Tom Sestito before ricocheting off T.J. Galiardi's skate and trickling into the net past Ilya Bryzgalov.
The goal initially was credited to Malone - it would have been the first of his career - before being awarded to Galiardi after officials had a chance to review the play.
Colorado's Gabriel Landeskog was in the penalty box with a double minor for high-sticking when the Flyers scored the game's first goal, but came back to even the score with his sixth goal of the season at 12:26 of the second.
Shane O'Brien fired a pass from the point to the slot, where Landeskog got his stick on the puck for a backhand shot that got past goalie Ilya Bryzgalov.
Landeskog was battling Kimmo Timonen for the puck along the boards when his stick flew up and struck the side of Timonen's head, drawing the double minor. The Flyers were on the first leg of the power play at 18:30 of the first when Jakub Voracek sent a pass across the slot to Scott Hartnell, who put the puck in an open net past goalie Jean-Sebastien Giguere.