Jim Harbaugh is owed more than a few mea culpas.

Many observers, including yours truly, felt benching Alex Smith and going with untested second-year quarterback Colin Kaepernick was a desperate, look-at-me moment by the San Francisco coach, a man engulfed by ego and intent on winning a particular way -- his way.

We were wrong.

Harbaugh has been a revelation since making the jump from Stanford to San Francisco, a 49ers mentor who's been a lot closer to Bill Walsh or George Seifert than Dennis Erickson, Mike Nolan or Mike Singletary.

Since arriving in Frisco to clean up Singletary's undisciplined mess, Harbaugh has quickly turned the Niners back into one of the NFL's elite teams, winning 2011 Coach of the Year honors for his work during his first year on the sidelines at Candlestick Park.

His second season will end at Super Bowl XLVII against his own brother, John Harbaugh, and the Baltimore Ravens.

Ten games into the younger Harbaugh's sophomore campaign, the 49ers were again atop the NFC West with an impressive 7-2-1 record. By that point, Harbaugh had lost only five times in 26 career regular-season games and already had a berth in the NFC Championship Game on his resume.

Little changed on a Monday night in late November when Harbaugh may have devised his best game plan to that point, turning Colin Kaepernick into Superman against the NFL's most opportunistic defense during an emphatic 32-7 Niners win over the Chicago Bears.

Expecting a run-first quarterback, the Bears were stunned to see a confident Kaepernick stand steady in the pocket and throw for two touchdowns in his first career start.

Playing in place of the injured Smith, who was still suffering from the effects of a concussion he sustained in the team's Week 10 tie against St. Louis, Kaepernick finished 16-for-23 for 243 yards and led the 49ers to scores on their first four possessions.

"They had a quarterback (Kaepernick) that hadn't played an awful lot but he was on and he looked like a seasoned vet from the start of the game," ex-Bears coach Lovie Smith said at the time.

Kaepernick's first game at the helm of the 49ers produced more yards and touchdowns than Joe Montana's and Steve Young's debuts combined.

Certainly a job well done by Kaepernick but it was time to pat the youngster on the head, tell him job well done and go back to the horse, who had won 20 of his last 26 games as San Francisco's starting quarterback, Smith.

Not so fast.

"We'll see," Harbaugh said when queried about who his signal-caller was going to be moving forward.

Benching a veteran quarterback who has led his team to the conference championship game the year before and had it comfortably atop its division seemed like an absurd thought.

And quarterback controversies are generally created by the media or fans -- not the head coach of a successful team.

Of course, in Harbaugh's mind -- there was no controversy. Smith was a game manager while Kaepernick brought, athleticism, a rocket arm and big play ability to his offense.

"I think quarterbacks that have a talent for running the ball can be very effective," Harbaugh said. "A quarterback that can get out of the pocket, run, pick up first downs, that's a threat that the defense has to account for. (Colin's) very good at reading and executing that type of offense."

That's an understatement.

Kaepernick's 10th NFL start will be at the Super Bowl in New Orleans.

For all the talk about how difficult read-option quarterbacks like Robert Griffin III and Russell Wilson have made things for opposing defenses, it's Kaepernick who has emerged as the best of the bunch, outdueling the reigning NFL MVP Aaron Rodgers and Pro Bowl fixture Matt Ryan in back-to-back starts during the postseason.

"He's acquitted himself really in every test he's been given," Harbaugh said. "A lot of people have talked about Colin. See how he does in this situation. See how the next game will prove something. We'll see how he does in the playoffs now. And see how he does in a road playoff. But, at every phase he's acquitted himself very well."

Kaepernick did it primarily with his legs against the Packers, amassing 181 rushing yards, an NFL record for a quarterback, and two touchdowns in the 49ers' 45-31 win. The University of Nevada product also completed 17-of-31 passes for 263 yards with a pair of scores to Michael Crabtree. In total, Kaepernick piled up 444 yards of offense in San Francisco's amazing 579-yard effort against Green Bay.

"He's that new-style quarterback in the NFL that can run the read-option, that can pull the ball down, run it and take it the distance from anywhere on the football field. Extremely strong-armed, accurate," said 49ers Pro Bowl safety Donte Whitner.

Atlanta tried to learn from the Packers' flawed defensive schemes in the NFC Championship Game, making sure its ends got up the field against Kaepernick in the read-option. The Milwaukee native, however, showed patience and handed the ball off inside to Frank Gore and the speedy LaMichael James when warranted while using his arm to stun the Falcons.

Despite falling behind 17-0, Kaepernick kept his cool, played a clean game and took what Atlanta gave him. Gore eventually ran for a pair of scores in the second half and the 49ers rallied past the Falcons, 28-24, securing their first Super Bowl appearance since 1994.

Kaepernick was limited to 21 rushing yards but finished 16-of-21 passing for 233 yards and a touchdown, finding tight end Vernon Davis five times for 106 yards and a TD.

"He just played great. He played great," Harbaugh said. "I don't even know the words to say it. I mean, it was a great performance by the quarterback."

And a great decision by Jim Harbaugh.

• Read more articles by John McMullen, Sports Network

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