Bergeron lost consciousness and was taken from the ice on a stretcher during the first period after he was hammered into the boards by Jones.
Bergeron was transported to Massachusetts General Hospital, where he was diagnosed by Bruins team physician Dr. Bertram Zarins.
Tests didn't show any other serious injuries to Bergeron's head or neck, and he was awake and able to move all his limbs, Zarins said.
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.
"Words really can't express the way that I feel right now. I am very apologetic for the hit and what I did," Jones said in a statement released by the team. "It was not intentional. It is something that I have never done before and it is not part of my character. I am extremely sorry.
"I hope he does OK and everything works out for him. I wish him nothing but the best in his recovery."
Bruins head coach Claude Julien called it "a dirty hit."
"I'm not saying he's a dirty player, all I'm saying is it was a dirty hit. We'll just have to let the league take care of it ... and hopefully they will," Julien said.
"This is the third major incident that club's had in 10 games. It's something that has to be addressed there."
Flyers 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 game, Flyers coach John Stevens defended the latest ugly hit by one of his players.
"That's just an innocent play by Randy Jones. I've had Randy Jones for a long time here. He's just going in there trying to defend and make contact and the last thing on his mind is trying to go run somebody and cause injuries," Stevens said.
The win snapped the Flyers' two-game losing streak and handed the Bruins their first home loss of the season.
Martin Biron stopped 38 shots - 32 of which were in the final two periods, raising his record to 7-2 - and Mike Richards had a short-handed goal for Philadelphia. Joffrey Lupol also scored.
"The first period was where we wanted to come out strong and we did," Biron said. "Even though we had only four shots, we had a few scoring chances and limited their scoring chances to the outside and gave us the rhythm that we wanted for the game."
Marco Sturm replied for Boston.
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 as he was treated.
As the whistle blew, Boston's Chuck Kobasew went after Jones, drawing a two-minute roughing penalty. Jones drew a five-minute major and a game misconduct.
After getting word of Bergeron's status, defenceman Andrew Ference said, "I guess that's obviously good news. It's nothing crazy serious for Patrice, but it's just another instance where you could just hit the replay on any comments that any other teammates have ever given after a play like that."
Sturm gave the Bruins a 1-0 lead in the second period with his fourth goal of the year.
Later in the second, Zdeno Chara failed to stop a pass at the point on a power play. The puck hopped over his stick and Richards picked it up on the fly. He slid a back-hander through the pads of Tim Thomas at the 9:36 mark for his sixth goal of the season, his second short-handed score.
The Bruins were called for too many men on the ice with 7:25 remaining in the second, and Lupol's fourth goal of the season came off a pass from Daniel Briere.
Thomas, who has allowed just eight goals in six starts, fell to 4-2.
Phil Kessel was awarded a penalty shot when Philadelphia defenceman Kimmo Timonen was judged to have thrown his stick as he dove to try to stop Kessel's shot. Kessel's penalty shot then went off Biron's upper arm.
"I thought our guys battled hard. I thought we probably deserved better," Julien said.
Notes: Flyers winger Simon Gagne missed his second straight game with dizziness. ... The short-handed goal was the ninth of Richards' career. ... The Bruins pushed the game time up three hours to allow local fans to watch Game 3 of the World Series on television. ... A large contingent of Flyers fans roared every time their team scored. ... Bruins rookie Milan Lucic played his 10th game, after the team had announced Friday he would be staying with the Bruins and not returning to his junior team in Vancouver. He had his fourth fight in 10 games.