The 49ers signed safety Tyree Robinson from the Dallas Cowboys practice squad to a two-year deal to take Garçon's roster spot.
Robinson will wear No. 49.
The team also signed tight end Marcus Lucas to the team's practice squad to replace tight end Cole Wick, who was signed by the Tennessee Titans.
Garçon has been dealing with the knee injury for most of the season. He missed his fourth-straight game on Sunday and his fifth during the past six games.
"We've waited on Pierre for a bit," head coach Kyle Shanahan told reporters on Monday. "It was going very positive for a while. That's why we felt real good about it. But, came back from that Bye week and it had gotten worse. We tried our hardest last week. He went out and went full-go Wednesday. It swelled up on him, caused him a lot of pain."
Garçon's 2017 campaign was cut in half when a neck injury forced the 49ers to place him on injured reserve on November 4, 2017.
The 49ers signed Garçon to a five-year deal on March 9, 2017. San Francisco has a potential out on his contract after this season.
"Now, I saw P in training camp when his knee wasn't bothering him," Shanahan continued. "He was playing at a high level. It's very hard to do that when you're not healthy, especially the age these guys are at.
"Hopefully, they can get healthy this offseason and then you've got to make decisions. You don't just get rid of people to get rid of people."
Shanahan and general manager John Lynch confirmed in October that the 49ers were fielding calls from NFL teams about a potential Garçon trade.
"I know there was a report on Pierre," Shanahan said on October 28. "That is true. He's one of the guys that people have asked about and we have talked about."
Obviously, nothing developed from those calls.
Garçon registered 24 receptions for 286 yards with one touchdown through eight games this season, his second with the 49ers. He has 64 catches for 786 yards with a single trip to the end zone during his time in San Francisco.
Garçon, an 11-year veteran, spent five seasons with the Washington Redskins and four with the Indianapolis Colts before signing with the 49ers.
The 49ers Communications staff provided the following rundowns of Robinson and Lucas.
Robinson (6-2, 202) originally signed with the Cowboys as an undrafted rookie free agent on May 11, 2018 out of the University of Oregon. He was active in each of the first two games of the season and was waived by Dallas on September 18. Robinson was signed to the Cowboys practice squad on September 20.
Lucas (6-4, 250) was originally signed by the Carolina Panthers as an undrafted free agent on May 16, 2014. Throughout his career, he has spent time on the practice squads with the Panthers (2014-15 & 2016), Miami Dolphins (2015), Chicago Bears (2015), Seattle Seahawks (2016), Indianapolis Colts (2017) and Oakland Raiders (2017). In 2018, he signed with the Detroit Lions on August 31 and was waived by the team on September 2. Lucas was signed to the Seattle Seahawks practice squad the following day and was later waived by Seattle on October 9.
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