Kaepernick, who was on the injury report Friday, told the 49ers that he wanted to undergo surgery on his left, non-throwing shoulder, prompting the team to put him on IR, a source told ESPN NFL Insider Adam Schefter.
There have been reports that Kaepernick has been dealing with a torn labrum in his left shoulder that could result in surgery next week. Kaepernick on Friday told the Sacramento Bee he initially suffered the injury in a Week 4 loss to the Green Bay Packers, a 17-3 defeat at Levi's Stadium in which Kaepernick was sacked six times and mocked by Packers linebacker Clay Matthews, who yelled, "You ain't Russell Wilson, bro."
But Kaepernick was not listed on an injury report until after the Niners' Oct. 22 loss to the Seattle Seahawks, in which he was sacked six times, and in that case, it was because of a right hand injury.
This week he was a somewhat surprise addition to the injury report, considering he was benched after a Nov. 1 blowout loss at the St. Louis Rams. The Niners originally had listed Kaepernick as probable for Sunday's game against the Seahawks as he was listed as a full participant in practice all week.
Undrafted rookie quarterback Dylan Thompson was promoted from the 49ers' practice squad Saturday to replace Kaepernick on the active roster and will serve as the backup to Blaine Gabbert.
The last-place Niners (3-6), who had a bye last week, benched Kaepernick for their Nov. 8 game in favor of Gabbert, who helped lead them to an upset victory over the Atlanta Falcons. Kaepernick played two snaps in that game, handing off and throwing a deep incompletion, while Gabbert was being checked on the sidelines after taking a hard hit.
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.
A second-round pick out of Nevada in 2011, Kaepernick took over in Week 11 of the 2012 season from a concussed Alex Smith and started 53 straight games, including the Niners' Super Bowl XLVII loss to the Baltimore Ravens and the following season's NFC title game loss to the Seahawks.
It was in that offseason when Kaepernick signed a $126 million contract extension that was lauded at the time as being very team friendly. While he is due to make $14.3 million in 2016 ($11.9 million in base salary, plus bonuses), $16.9 million in 2017, $17.4 million in 2018 and $19.2 million in 2019, per ESPN Stats & Information, the guarantees do not vest until April 1 of each calendar year.