Kaepernick made the move look like a stroke of genius as he wrote a brilliant opening chapter to his playoff career with a record-breaking performance in a 45-31 victory over the visiting Green Bay Packers on Saturday.
The strong-armed quarterback set a National Football League standard for rushing by a quarterback by gaining 181 yards on the ground including touchdowns covering 56 and 20 yards.
The 25-year-old Kaepernick terrorized the team he grew up cheering for as a boy in Wisconsin before his family moved to California.
"It's been amazing," the 2011 second-round draft pick out of the University of Nevada-Reno said. "I couldn't ask for anything more."
He also threw a pair of touchdown passes to Michael Crabtree and had 263 passing yards for 444 yards of total offense that impressed Packers' quarterback Aaron Rodgers, the reigning NFL Most Valuable Player.
"He was running all over the field," said Rodgers, who led the Packers to the Super Bowl title two years ago.
"He's big, strong, athletic, throws the ball well, runs the ball extremely well. We didn't really have a whole lot of answers for him."
Harbaugh had to answer wave after wave of questions when he installed Kaepernick as his regular quarterback after Smith, the 2005 top pick of the NFL Draft, had recovered from a concussion after missing one game.
The 49ers coach saw Kaepernick and his big-play ability as the quarterback of the future who was ready to take over for the steady, but unspectacular Smith, who steered the team into the NFC title game last season.
Kaepernick passed his first post-season test with flying colors and shared the credit.
"Our offensive line played great today. They did a lot of good things up front. Our running backs ran well and our receivers made plays," said the 6-foot-5 Kaepernick, who eats up yards with his long strides.
"It's a lot easier on me when other people are making plays."
Kaepernick threw an interception on his second pass of the game that turned into a 52-yard return by Sam Shields for a Green Bay touchdown, but quickly recovered his composure.
He led San Francisco on an 80-yard drive on the next series, tying the game 7-7 on a 20-yard touchdown run.
Kaepernick's 56-yard touchdown run in the third quarter after a fake hand-off put the Niners out in front for good.
With his best previous NFL rushing effort the 84 yards he gained last month against the St Louis Rams, Kaepernick said he did not consider himself as a running quarterback.
"I don't want to be characterized," he said, adding that he figured he would have opportunities to run against Green Bay.
"We had a lot of plays we put in to try and utilize that, and also open up running lanes for our running backs. It was just another tool for this offense."
(Reporting by Larry Fine in New York; Editing by Alastair Himmer)