He was activated from the physically unable to perform list and added to the 53-man roster. The Niners waived linebacker Shayne Skov on Saturday to make room for Kilgore. San Francisco plays at Chicago on Sunday.
Kilgore hasn't played since breaking his left leg against the Broncos in October 2014.
Kilgore, who has appeared in 40 games since he was drafted by the 49ers in 2011, won the starting job at the beginning of last season. He made seven starts before his injury.
Skov appeared in the first 11 games this season and registered four tackles on special teams.
AP NFL website: www.pro32.ap.org and www.twitter.com/AP-NFL