Kaepernick started the last two San Francisco games in place of the injured Alex Smith and played well, earning a start Sunday at St. Louis.
The 49ers defeated Chicago (32-7) and New Orleans (31-21) in their last two games, and Kaepernick was a combined 32-of-48 for 474 yards, three touchdowns and one interception.
But with Smith recovered from the concussion he suffered Nov. 11, there was a question as to whom the 49ers would start. Harbaugh ended the suspense Wednesday.
"We believe Colin has the hot hand and we're going with Colin," Harbaugh said.
Smith has been the 49ers' starting quarterback virtually his entire seven-year NFL career, starting 75 of his 79 games played. In nine games in 2012, he is 152-of-217 for 1,731 yards, 13 touchdowns and five interceptions.
San Francisco (8-2-1) leads the NFC West by 2 1/2 games. Only the 10-1 Atlanta Falcons have a better record in the conference.