Kaepernick, who underwent surgery to repair a torn labrum in his left (non-throwing) shoulder on Nov. 24, is due a guaranteed $11.9 million if he is still on the Niners' roster on April 1.
Kaepernick, whose play has declined over the past two seasons, was placed on injured reserve after being demoted in favor of Blaine Gabbert, who is 1-2 since replacing him.
The timetable for Kaepernick's recovery is expected to be four to six months.
Congrats to Blaine and the rest of the team on the great road win! Keep Rollin!— Colin Kaepernick (@Kaepernick7) December 6, 2015
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 for 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.
ESPN Staff Writer Paul Gutierrez contributed to this report.