Bergeron was chasing a loose puck in the Flyers zone during the first period when Jones chased him down and drove his head into the boards.
The 22-year-old crumpled to the ice while the Bruins went after Jones, 26.
Emergency staff immediately came out to tend to Bergeron, immobolizing him and being very careful not to move his head.
He was carted off the ice and taken to hospital.
There was no immediate word on his condition.