Kaepernick also did not take part in team drills during Thursday's practice. The team called it a "planned day of rest" for the quarterback.
Kaepernick is involved in a quarterback competition with Blaine Gabbert, who received the majority of the reps on Thursday and will get the majority again on Friday. Prior to Thursday, Kaepernick and Gabbert were receiving a relatively equal share of reps during training camp practices.
The 49ers have not yet named a starter for Sunday's exhibition opener against the Houston Texans. They are expected to make a decision sometime following the team's joint-practice.
Kaepernick was one of the players that was scheduled to meet with the media following Friday's practice. It is unknown if that will still occur.