In a corresponding move, the 49ers also promoted quarterback Nick Mullens from the practice squad to the active roster. He will wear number 4.
The team also announced the signing of defensive lineman Ryan Delaire, offensive lineman Christian DiLauro, and defensive back Dexter McCoil to the practice squad.
The Delaire signing was already reported by the San Francisco Chronicle.
Garoppolo will undergo surgery once the swelling in the knee goes down, which is the typical process for an ACL injury. There doesn't appear to be further damage to his left knee other than to the ACL.
"None specific that I've been told," head coach Kyle Shanahan said on Monday. "But I don't think you ever know for sure until you open it up. It seems kind of like with all ACLs there's always some other stuff in there. The message I got today was that it was fairly good news, relatively speaking."
Garoppolo's season ended after just three games. He completed 59.6 percent of his passes for 718 yards with five touchdowns and three interceptions this season. That followed up a 2017 campaign that saw Garoppolo join the 49ers at the trade deadline, start and win the final five games of the year, and pass for 1,560 yards with seven touchdowns and five interceptions during his six appearances.
The New England Patriots made Garoppolo a second-round draft pick out of Eastern Illinois in 2014. The 49ers acquired him from the Patriots on October 30, 2017, in exchange for a second-round draft pick.
Garoppolo is expected to be healthy by the start of next season.
"I know I'm extremely excited about Jimmy being here next year," Shanahan said. "Jimmy is a very talented quarterback. He's played at a high level in the games that he has played."
The 49ers signed Mullens as an undrafted free agent out of Southern Miss in 2017. He spent all of last season on the practice squad and was signed to a reserve/future contract on January 2.
"Right now, our plan is to bring Nick up (to the active roster) so we have two (quarterbacks) at least right away," head coach Kyle Shanahan said on Monday.
Mullens completed 72.1 percent of his passes for 396 yards with a touchdown and three interceptions during the 49ers' four preseason games in August. He also ran the football five times for 20 yards and two scores.
Mullens completed 60 percent of his passes for 11,994 yards with 87 touchdowns and 46 interceptions in four seasons with the Golden Eagles.
The Cleveland Browns signed DiLauro as an undrafted free agent out of Illinois on May 4 and then waived him on September 1 before briefly signing him to the practice squad. Cleveland released him on September 4.
The 49ers initially claimed McCoil off of waivers from the Los Angeles Chargers on October 9, 2017. He appeared in eight games for San Francisco and registered a tackle. The 49ers waived McCoil on April 30, re-signed him on August 17, and then released him again on September 1.
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