Quarterback Dylan Thompson was promoted from the practice squad to the active roster to take Kaepernick’s spot.
Kaepernick was recently benched in favor of Blaine Gabbert as the starter. Just Friday, Kaepernick was listed as probable on the 49ers’ injury report.
According to the Sacramento Bee, he has had the injury since the team’s Oct. 4 loss to the Green Bay Packers.
Kaepernick played in nine games (eight starts) this season. He threw for 1,615 yards with six touchdowns and five interceptions. He also rushed for 256 yards with one touchdown.
San Francisco (3-6) visits the Seattle Seahawks (4-5) on Sunday.
Romo was taken off the team’s injured reserve/designated to return list on Saturday. He has been out since breaking his left collarbone on Sept. 20 against the Philadelphia Eagles.
The Cowboys won their first two games of the season but have lost all seven that Romo has missed.
Quarterback Aaron Rodgers was listed as probable on Friday with a sore right shoulder, appearing on the injury report for the first time this season.