Kaepernick was listed on the team's Week 11 injury report as probable with a left shoulder injury. He hurt the shoulder in Week 4, but started the next four games.
NFL Media Insider Ian Rapoport reported Kaepernick will have surgery on his non-throwing shoulder on either Monday or Tuesday, per a source.
The quarterback was benched in Week 9 in favor of Blaine Gabbert. Coach Jim Tomsula said at the time he wanted Kaepernick to take a step back and breathe. The prevailing thought was Kap had a chance to regain the starting gig.
That chance is now gone and he'll have the rest of the season to watch Gabbert guide the Niners.
The move puts Kaepernick's future in San Francisco in question.
The quarterback signed a team-friendly deal in 2014 that allows the 49ers to walk away from the 28-year-old Kaepernick. His $13.9 million salary for 2016 doesn't become guaranteed until April 1.
Kapernick struggled this season as a pocket passer, lacked accuracy and touch, and his field vision was troubling.