Garçon did not play during Sunday's victory against the Denver Broncos. It was his fourth-straight missed game and his fifth in six games.
"We've waited on Pierre for a bit," Shanahan said. "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.
"After having that same thing through almost most of the year, especially it was the week before the Green Bay game that it really started coming, it was just lingering too long where P knew he had to get something done, a scope. So, we had to shut him down."
The 49ers signed Garçon to a five-year deal on March 9, 2017. San Francisco has a potential out on his contract after the season.
Garçon ends the season with 24 receptions for 286 yards with one touchdown through eight games.
Shanahan said defensive end Cassius Marsh is in the concussion protocol. Cornerbacks Ahkello Witherspoon (ankle) and Tarvarius Moore (shoulder) are day-to-day as the team prepares for its second bout against the Seattle Seahawks.
The 49ers will re-check running back Matt Breida (ankle), safety Jaquiski Tartt (shoulder), cornerback K'Waun Williams (knee), and linebackers Mark Nzeocha (groin) and Malcolm Smith (Achilles) on Wednesday before the team's first practice of the week.
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