In his two years as an NFL head coach, Jim Harbaugh has yet to make a mistake. He inherited a 6-10 team from Mike Singletary, and promptly spun that into a 13-3 squad that made it to overtime of the NFC championship game in 2012. Harbaugh has been lauded for the way he treats players, conducts practices, and prepares his team each week. He’s a guru when it comes to play design, as San Francisco’s offense always seems to keep the defense guessing.

So when Harbaugh opted to stay with Colin Kaepernick’s “hot hand” after a Week 11 win over Chicago instead of returning to the incumbent Alex Smith, Niners fans (myself included) should have given him the benefit of the doubt.

But at the time, it seemed like a very brash decision. Kaepernick had picked apart the Bears, but all his deep throws came against single coverage and he missed a few easy ones. A week earlier when he replaced Smith mid-game against the Rams, he missed badly on some very simple throws. Kaep has incredible tools (arm strength and running ability), but there was a legitimate argument that he was a high risk, high reward player. With the best defense in football, San Francisco didn’t need to take risks. Kaepernick has a much higher ceiling than Smith, but did he give the 49ers the best chance to win it all this year?

The case for Alex Smith to keep his job was quite compelling. Smith was red hot when he suffered his concussion. He had completed 25 of his last 27 passes for four touchdowns and zero interceptions over a two-and-a-half game stretch when he went down. It’s hard to play the position of quarterback much better than that. At the time of his injury, Smith was second in the league in QB rating, and he was putting up career-high stats across the board. After having seven different offensive coordinators in seven years, limited supporting talent, and a porous offensive line, Smith was finally in a position to succeed and he was making huge strides. He also finally had two straight offseasons with the same playbook, and that familiarity was paying dividends.

A quote from Smith’s college coach Urban Meyer came to mind as he was showing signs of reaching the upper echelon of NFL quarterbacks:

“Alex is an extremely quick learner. However, he’s a guy that, until he understands it, he is nonfunctional. He is a guy that — I keep hearing how Brett Favre kind of makes something out of nothing and is a person that runs around to make a play — Alex Smith is not that kind of player. Alex Smith is a person that, once he is taught, has to learn it all. He might struggle early, but once he gets it, he gets it.”

Smith never had the chance to succeed early in his career because there was so much coaching turnover and so little talent around him. Just at the moment when Smith seemed to be hitting his stride, the rug was pulled out from under his feet. The one game he missed cost him his job. Naturally, there were many 49ers fans that were skeptical of this decision. As Kaepernick said after the NFC championship game, “there were a lot of people that didn’t believe I was capable of leading this team.” He’s right, but fortunately for him, the only person that mattered – Jim Harbaugh – believed in him.

Harbaugh clearly had this move in mind for a long time. You don’t bench the second highest rated QB in the league unless you strongly believe that you have something better behind him. Harbaugh knew he had something special in his backup QB, and it took some serious stones to go with the unproven second-round pick from Nevada.

The rest of the league has now seen what Harbaugh saw in practice – arguably the best raw talent at QB in the NFL. Kaepernick has the speed of Michael Vick, the arm strength of John Elway, and his maturity belies his years of experience in the pros. Critics of running quarterbacks and critics of the option play will say the 49ers’ style of offense isn’t sustainable because the QB takes too many hits. However, on 50+ option plays this season, Kaep has only been hit six times. He became very familiar with running option plays when he was at Nevada and leading Chris Ault’s “pistol” offense. That experience meant Kaep hit the ground running when he was given the reins to San Fran’s offense.

The 49ers are lucky to have such an incredible talent at the most important position on the field. But they are even luckier to have a head coach who turns anything he touches into gold. Harbaugh should be credited for making a very bold and controversial decision. He didn’t have to make a change at QB, but his switch has given San Francisco a weapon that might put them over the top for their sixth Super Bowl title. I’m still waiting for Harbaugh to make a mistake as an NFL head coach, and it’s gotten to the point where if he told me to jump off a bridge, I would seriously consider the benefits of such a move.