Brad Marchand picked a perfect time to snap his scoring slump.
Nathan Horton also scored to help the Northeast Division-leading Bruins clinch a playoff spot. Marchand's goal was his 20th and first in 13 games.
“There's been pressure on him to get the 20th and a great way to get it is a game winner,” said Mark Recchi, who assisted on the goal.
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.
The two teams could be headed for a playoff rematch. Last spring, the Flyers become the third NHL team in history to overcome a 3-0 series deficit when they beat the Bruins to advance to the conference finals.
“It's going to be very interesting,” Marchand said. “Every game determines who we're going to play. It's going to be exciting watching every game because it could determine the outcome of where we're at in the playoffs.”
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.
“We were patient and disciplined,” said Tim Thomas, who made 27 saves for the Bruins. “They took the penalty at the end and we capitalized.”
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.
But the Flyers, coming off a 4-1 win at the New York Islanders on Saturday night, looked sluggish the rest of the way.
“First period, we had some passions, some energy,” defenseman Andrej Meszaros said. “Then it disappeared for some reason. They did everything better than us.”
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.
The Flyers went 0-1-2 against the Bruins, Capitals and Penguins in the past week.
“It's just little things we need to correct,” Richards said. “We need to be more consistent.”
Boston is four points out of second place in the East.
“We're focused on where we are and not where we're going to be,” Recchi said.
“We're pretty confident we're not going to slip past third. We just want to be playing our best hockey full speed ahead.”