Smith won plaudits last season after throwing for 3,144 yards and 17 touchdowns and leading the 49ers to the NFC Championship game where they lost to eventual Super Bowl winners the New York Giants.
After an equally strong start to the current season, where he had thrown for 1,737 yards in nine starts with 13 touchdown passes, Smith suffered a concussion against the St. Louis Rams.
In stepped Kaepernick, who led the 49ers through the remaining seven regular season games, throwing for 1,814 yards and 10 touchdowns, and to a Feb. 3 Super Bowl showdown with the Baltimore Ravens in New Orleans.
"I would be lying if I said it wasn't a little bittersweet," Smith told the San Jose Mercury News on Wednesday.
"Yes, I want to be out there. It's what you work for coming into the season. That was the mindset, the goal for me."
Despite Smith's swift return to full health, 49ers coach Jim Harbaugh decided to stick with 25-year-old Kaepernick, who impressed with his mobility, poise and arm strength.
It was a controversial decision, a risky move in the eyes of many, but few would argue that Harbaugh made the right choice after Kaepernick's masterful performances in play-off wins over Green Bay and Atlanta.
Smith said injuries were part and parcel of the game and back-ups only get the chance to shine when the starter goes out.
"It's the nature of sports. He got an opportunity, stepped up and made the most of it," he added.
"That's the deal. That is how I get my start in college. It was no different. The guy in front of me got hurt and I got my first start."
Kaepernick has certainly taken his chance and Smith says he has shown his qualities in abundance.
"No question, you see the playmaking ability on the practice field. You saw it in pre-season. The thing I'm shocked by is the consistency," he said.
Despite having to watch from the sidelines, Smith shared in his team mates' success.
"You go through so much together, especially these guys who have been here a chunk of time," he said. "If you can't be happy there is something wrong with you."
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