Nathan Horton also scored to help the Northeast Division-leading Bruins clinch a playoff spot.
The Eastern Conference-leading Flyers had been unbeaten in regulation in their previous nine games. They are two points ahead of Washington and Pittsburgh for the top spot.
Kris Versteeg scored for Philadelphia.
With Flyers captain Mike Richards in the penalty box for high-sticking, Marchand stuffed a rebound off a slap shot by Dennis Seidenberg past Brian Boucher. It was Marchand's 20th goal and first in 13 games.
Tim Thomas made 27 saves for the Bruins.
Versteeg opened the scoring early in the first with his 20th goal. His one-timer from the side of the net off a pass from Richards beat Thomas to the stickside.
The Bruins tied it on Horton's 23rd goal in the second. Just 4 seconds into a power play, Horton put in a rebound off a slap shot from the point by Tomas Kaberle.
Thomas went down to his knees to block a point-blank shot by Jeff Carter early in the third to keep it tied.
NOTES: The Bruins are 7-0-1 in Philadelphia since March 10, 2007. ... The Flyers are 13-6-5 without D Chris Pronger this season. He's sidelined by a hand injury. ... The Bruins are 3-0-1 against the Flyers this season. They're one of only two teams with a winning overall record (90-56-27) against the Flyers. Montreal is the other. ... Thomas is 10-2-2 against Philadelphia.