He then sustained a concussion in the second quarter of a 24-24 tie against St. Louis on Nov. 11 — saying later he threw a touchdown pass with blurry vision. Smith sat out the next game as Kaepernick dazzled in his debut as an NFL starter, beating the Bears handily at home on Monday Night Football.
After that, Harbaugh vowed to stick with the "hot hand," as he regularly put it, while complicating matters by still referring to Smith as a starter.
Smith's most poignant response to the situation was, "I feel like the only thing I did to lose my job was get a concussion."
Kaepernick led the 49ers to the NFC championship and a 34-31 loss to Baltimore in the Super Bowl in his second season. Now the 49ers are looking for his backup.
The 28-year-old Smith struggled for most of his career in San Francisco, plagued as much by coaching and constant coordinator changes as by his own indecisiveness. But when Harbaugh became coach in January 2011, Smith blossomed under the former QB's guidance. He was among the league leaders in passer rating (104.1) with a 70.2 completion percentage when he got hurt last season.
Fox Sports first reported the deal Wednesday.
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AP Pro Football Writer Barry Wilner and AP Sports Writer Dave Skretta contributed to this story.
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