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.
The 49ers' perfect Super Bowl record? That's over, too. They lost for the first time in the championship game.
Perhaps it's a bit premature to begin talking Bay Area dynasty again — in football, at least.
Playing for a title for the first time since Hall of Famers Steve Young and Jerry Rice won with a rout of San Diego 18 years ago, Jim Harbaugh's Niners made costly mistakes on both sides of the ball early in the game. And special teams, too.
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. His off-balance throw under pressure on fourth down sailed through the end zone. Kaepernick lowered his head slightly and walked slowly off the field.
No comeback this time in the Big Easy.
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.
The 25-year-old completed 8 of 13 first-half passes, was sacked twice and threw an interception as San Francisco fell behind 21-6.
In the NFC championship game at Atlanta two weeks ago, such a deficit was no problem. Kaepernick rallied the Niners back from 17-0, while the defense delivered by holding the Falcons scoreless in the second half to win 28-24.
On Sunday, Kaepernick led his team into the end zone for the first time with 7:20 remaining in the third quarter after the power outage when he found Crabtree.
But a stingy San Francisco defense that relied on its ball-hawking, run-stopping play all season, couldn't consistently slow down Flacco and the high-powered Ravens.
Leading up to the Super Bowl, Kaepernick had handled himself beautifully in hostile environments — beating Drew Brees and the Saints right here in the Superdome on Nov. 25, and later guiding the Niners at New England. And, of course, the win against the Falcons on Jan. 20 that returned San Francisco to the Super Bowl at last.
The 49ers were hoping for their own downtown victory parade and to have the World Series champion Giants take part after Harbaugh and quarterback Alex Smith drove in the San Francisco baseball team's parade last fall.