Kaepernick, who was on the injury report Friday, told the 49ers that he wanted to have surgery on his non-throwing shoulder, prompting the team to put him on IR, a source told ESPN NFL Insider Adam Schefter.
The Niners originally had listed Kaepernick as probable for Sunday's game against the Seattle Seahawks. Undrafted rookie quarterback Dylan Thompson was promoted from San Francisco's practice squad Saturday to replace Kaepernick on the active roster.
There's been lots of speculation Kaepernick and the 49ers have no choice but to part ways after this season, but this injury could affect that. He will need to pass a physical prior to April 1 or it's possible he could remain a 49er in 2016. The team benched Kaepernick for their Nov. 8 game in favor of Blaine Gabbert, who helped lead San Francisco to an upset victory over the Atlanta Falcons. Kaepernick, 28, completed 59 percent of his passes this season for 1,615 yards, six touchdowns and five interceptions. His 78.5 passer rating is the fifth-lowest in the NFL among qualified quarterbacks. Looks like Gabbert may finish out the year as the starter, but with the offense banged up with injuries, there's not a lot of fantasy upside for Gabbert.