The 49ers have placed quarterback Colin Kaepernick on the injured reserve list and promoted rookie Dylan Thompson to the active roster from the practice squad, the team announced on Saturday.
Reports earlier this month suggested Kaepernick would not return to San Francisco in 2016 due to a frayed relationship between him and the team's upper management.
Kaepernick had been listed as probable on the team's Week 11 injury report with a left shoulder injury after getting hurt in Week 4.
He is now expected to undergo surgery on his non-throwing shoulder.
After a disappointing start to the season, Kaepernick will finish with 1,615 yards and six touchdowns while adding 45 carries for 256 yards rushing and one touchdown on the ground in nine games.
Thompson, 24, signed with San Francisco as an undrafted free agent out of South Carolina in May and was released by the team on September 5 before signing to the 49ers' practice squad the following day. He set the Gamecock passing yard record and led the SEC with 3,564 last season.