That turned out to be a major roll of the dice — maybe the biggest in the league this season — and whether it was a wise move is still up for debate. The determining factor will be how well Kaepernick plays in the postseason, which for the 49ers begins Saturday night against Green Bay at Candlestick Park.
"Jim went all in, that's his nature," said ESPN's Steve Young, who in the early 1990s took over as quarterback of the 49ers from Joe Montana. "So when Colin played well in Chicago [in a 32-7 victory over the Bears on Nov. 19], Jim's reaction was, 'I've been looking for this.' … I don't think he looked back."
Smith led the 49ers to the doorstep of the Super Bowl last season, directing a home victory over New Orleans in the divisional round before losing in overtime to the visiting New York Giants in the NFC championship game.
Saturday, the 49ers and Packers will meet for the sixth time in the postseason, with Green Bay holding a 4-1 edge in the previous playoff games.
Facing the Packers is especially meaningful for Kaepernick, who was born in Milwaukee and lived in Fond du Lac, Wis., before moving to California at 4. He was a Packers fan as a kid, and a Brett Favre fan in particular.
"He was just a playmaker," Kaepernick said. "He wasn't afraid to take chances. He was passionate about the game and he was going to do anything he could to help his team win."
Now, Kaepernick has the chance to do the same in the biggest game of his career. The choice to switch to Kaepernick is more evidence that Harbaugh is anything but risk-averse.
Kaepernick, a second-round pick of the 49ers in 2011, got the starting nod as a fill-in for Smith, who had suffered a concussion against St. Louis. In the eight quarters that preceded that injury, Smith completed 32 of 35 passes for 385 yards with five touchdowns, an interception, and a passer rating of 140.2. In other words, he had more touchdowns than incomplete passes.
And with Smith at quarterback on this season's kickoff weekend, the 49ers beat the Packers, 30-22, at Lambeau Field.
But based on a feeling he had, Harbaugh stuck with Kaepernick, who's more mobile and has a greater potential for explosive plays.
"It was not a predetermined move," Harbaugh said this week, adding: "It's pretty well-documented how we feel about both guys, that one's our left arm, one's our right arm. And both are very good quarterbacks. And we felt we could win with either quarterback. And we're in a great situation having both those men on our team."
Although Smith played brilliantly in last season's divisional win over the Saints, the 49ers' offense ground to a halt in the championship game, when the San Francisco wide receivers combined for one catch. Upgrading that position was a priority in the off-season, with the team drafting receiver A.J. Jenkins in the first round (he's been a non-factor), and signing free agents Mario Manningham (now injured), and Randy Moss.
So successful was the team last season, the bar has been raised. Harbaugh, named the NFL's coach of the year in his debut season a year ago, is the eighth head coach since 1970 to win a division title in each of his first two seasons.
If Kaepernick were to struggle against the Packers, Harbaugh's decision to keep Smith on the bench would be dusted off, put under the microscope, and examined from every angle.
Kaepernick has put up impressive numbers in his seven starts. He has completed 136 of 218 passes (62.4%) for 1,814 yards with 10 touchdowns and three interceptions. He has run for 415 yards and five touchdowns.
"I applaud Jim Harbaugh for making the decision when he did, because it wasn't an easy decision to make," said Hall of Fame quarterback Troy Aikman, now a Fox analyst. "The easy thing to do would have been to go back to Alex Smith, and it wouldn't necessarily have been the wrong decision because Alex was playing really good football."
Harbaugh chose the path of greater resistance, and in the process bumped up the stakes.
"If it all blows up on Saturday, that will take a lot of goodwill out of the bank," Young said. "Now, that doesn't change much. I mean, [Harbaugh] is still going to be around, still going to be a great coach. But it's a high-risk situation.
"And where there's high risk, there's high reward."