Ilya Bryzgalov made 22 saves in his first game for the Flyers since signing a nine-year, $51 million contract.
Reigning Vezina Trophy and Conn Smythe Trophy winner Tim Thomas stopped 27 shots for Boston.
Claude Giroux and Jakub Voracek scored 47 seconds apart in the final minute of the first period for the Flyers, who overhauled their roster after being swept out of the playoffs by Boston in the second round. The Bruins went on to win their first Stanley Cup title since 1972.
Brad Marchand scored for Boston.
The loss to the Bruins in the Eastern Conference semifinals sent the Flyers scrambling to rebuild in the offseason. Eight players in uniform on Thursday night were playing their first game for the team - including three rookies - and among them was Jagr, the 39-year-old former Penguins star who is the NHL's leading scorer among active players and ninth overall.
The Flyers also acquired the rights to Bryzgalov and signed him to a big deal to replace the ineffective rotation they have used for the past several years. Gone were offensive stars Mike Richards, their former captain, and Jeff Carter, last season's team-leading goal scorer.
Richards and Carter were traded on the same day in separate stunning deals, in part to create salary cap room to sign Bryzgalov.
The defending NHL champion Bruins were largely intact, with the notable departures of Mark Recchi to retirement and Michael Ryder and Tomas Kaberle as free agents. Defenseman Joe Corvo was the major acquisition.
Before the game, the Bruins brought out members of the 1972 Cup-winning team, including Bobby Orr, to help raise the 2011 championship banner to the rafters.
The emotional ceremony led right into the game, and Marchand, a surprising star in Boston's Cup run, scored a power-play goal midway through the first period on a pass from Tyler Seguin to give Boston a 1-0 lead.
But the Flyers answered with two in the final minute of the first, including Claude Giroux's goal off an assist from Jagr with 50 seconds left. With just 2.4 seconds remaining in the period, Voracek gave Philadelphia a 2-1 lead with a shot through Thomas' legs.
Bryzgalov and Thomas shut things down from there.