Kilgore was injured in the third quarter and was seen with a cast on his left leg after the game.
He has started all seven of San Francisco's games this season after taking over the starting position during training camp.
"It's always tragic to lose a player," 49ers quarterback Colin Kaepernick said, according to CSN Bay Area. "I don't know exactly what it is right now. Hopefully it's not something that is season-ending."
Undrafted rookie Dillon Farrell replaced Kilgore in the lineup and also left the game after injuring his ankle. Farrell's ankle injury is not considered serious.
No word on who will replace Kilgore for the long term, but Farrell or rookie Marcus Martin, a third-round draft pick, could get the nod in San Francisco’s next game, which is Nov. 2 at home against the St. Louis Rams.
Kilgore is in his fourth season with the team after being selected in the fifth round of the 2011 NFL draft. He signed a three-year contract extension in the offseason, averaging $1.8 million a season.
- Scooby Axson