Harbaugh, however, made sure to point out that nothing was "set in stone."
The dual-threat quarterback out of Nevada shined in this week's preseason game, where he ran for 92 yards on three carries, including one touchdown run of 78 yards. He went for 40 yards on 5-of-9 passing on Friday, a 17-6 win over the Minnesota Vikings.
In his rookie season with San Francisco, Kaepernick played in three games and only threw five passes.
Kaepernick has now separated himself from Scott Tolzien and Josh Johnson, who were also vying for the second-string spot. Harbaugh said that all four quarterbacks will play on Saturday, when the 49ers face the Houston Texans.