Said 49ers head coach Kyle Shanahan: "With Jimmy we're fearing ACL. We'll find out tomorrow. I haven't had a chance to talk to him yet. I feel for him."
Garoppolo will undergo an MRI on Monday to assess the severity of the injury, according to Mike Garafolo of NFL Network.
A serious injury could be devastating for San Francisco after the quarterback's meteoric rise over the past year.
The former New England Patriots backup made only two starts in three-and-a-half seasons with the Pats but found new life after being traded to the Niners last season. He transformed San Francisco on the field, going 5-0 as a starter and posting a 96.2 quarterback rating, and was rewarded in the offseason with a five-year, $137.5 million contract.
Garoppolo has taken advantage of the opportunity, totaling 718 passing yards and five touchdowns with three interceptions through three games in 2018.
If Garoppolo misses time, the 49ers will have to try to survive with C.J. Beathard at quarterback.