"We were ready for the second half," Kaepernick said. "We knew we had to score to get back in the game. We had good plays, we had bad plays in the red zone."
No team has come from more than 10 points down to win a Super Bowl, and Kaepernick had a chance to make it happen less than three months after becoming San Francisco's starter.
He regrouped during a 34-minute delay early in the third quarter because of a power outage, finding his groove and turning the Super Bowl into a wild game down the stretch and gave yet more cred to the pistol offense designed by his old college coach that is so well suited for the NFL's young, mobile quarterbacks.
"Colin was cool the entire game," left tackle Joe Staley said. "Colin was the same he's been the whole entire season. He's never shown any hints of being rattled, any hint of being uncomfortable on the football field, and he showed that exact kind of character today."
Kaepernick directed four second-half scoring drives, throwing a 31-yard touchdown pass to Michael Crabtree and also running 15 yards for a TD. But the 49ers missed the two-point conversion that would have tied the game with less than 10 minutes left.
Crabtree didn't get much help in a mistake-filled first half by San Francisco (13-5-1), which failed to stop Joe Flacco and deliver the franchise's sixth championship that would have matched the Pittsburgh Steelers for most ever.
Yet Kaepernick did a little bit of everything in San Francisco's final drive, when the 49ers got the ball back at their own 20 with 4:19 remaining and trailing 34-29. He ran for 8 yards, hit Crabtree on a 24-yard gain and handed off to Frank Gore for a 33-yard run to the Baltimore 7.
But with three chances from the 5, Kaepernick threw three straight incomplete passes intended for Crabtree, who got tangled up with a defender on the final play but no holding was called Harbaugh screamed from the sideline and signaled for a penalty.
Kaepernick's off-balance throw under pressure on fourth down sailed through the end zone. Kaepernick lowered his head slightly and walked slowly off the field.
"That wasn't the original option," Kaepernick said. "It's something I audibled to at the line based on the look they gave us."
Kaepernick wound up 16-for-28 for 302 yards with three sacks and an interception for a 91.7 passer rating in his outstanding Super Bowl debut. The interception was the first by the 49ers in six Super Bowls and ended a streak at 169 passes without one.
Kaepernick also rushed for 62 yards, joining Joe Montana as the only quarterbacks to pass for 300 yards and run for 50 in a Super Bowl.