Bergeron was chasing after a loose puck in the Flyers zone late in the first period when Jones closed in on him and drove his head into the boards with his forearm.
The 22-year-old crumpled to the ice and lay on his back motionless while the Bruins went after Jones, 26.
Medical personnel cut away Bergeron's jersey and shoulder pads as they worked on him, placing his neck in a brace.
They placed him on a board and then onto a stretcher, his legs taped together and his arms folded across his chest. There was little sign of movement. The game was delayed some 15 minutes.
There was no immediate word on his condition.
Jones was assessed a five-minute major and game misconduct at 16:07.
Jones' hit is the latest violent incident involving the Flyers this season.
Prospect Steve Downie was suspended 20 games after a hit to the head of Ottawa Senators forward Dean McAmmond in an exhibition contest. Then on Oct. 10 in Vancouver, Jesse Boulerice laid a vicious cross-check to the mouth of Canucks centre Ryan Kesler that resulted in a 25-game suspension.
After the Boulerice incident, the Flyers found themselves fighting off an emerging perception that they were a team full of out-of-control goons.
"I think we're in agreement that there's no place in the game for this anymore," general manager Paul Holmgren said Oct. 12. "I do think it was an isolated incident."
Added head coach John Stevens: "It's almost implied that's the direction we're going when it couldn't be further from the truth."