Following a power outage, it was Kaepernick whose personal flood lights kicked on.
Kaepernick dashed away from pursuit on a 15-yard touchdown run to the left in the fourth quarter to close the Ravens' advantage to 31-29.
On the ensuing two-point conversion try, though Kaepernick threw incomplete to wide receiver Randy Moss.
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Veteran safety Ed Reed, a native of St. Rose, La., forced Kaepernick to throw it too early to have a shot at picking up the conversion.
But Kaepernick kept peppering the Ravens with crisp spirals, finishing the game 16 of 28 for 302 yards, with one touchdown, one interception and a 91.7 quarterback rating.
He rushed for 62 yards on seven carries and the one score.
"He's something special," outside linebacker Courtney Upshaw said. "We came out with the mindset that it was love. We stuck together. We preached that."
It was an entirely different story in the first half, one where Kaepernick was effectively stonewalled. He completed just 8 of 13 passes in the first half as he was sacked twice by outside linebacker Paul Kruger.
Kaepernick was under plenty of duress, and was intercepted once by Reed on a pass meant for tight end Vernon Davis.
Ultimately, the Ravens' defense remained true to form to the very end.
They beat the 49ers after a rocky span against Kaepernick, one of the most talented young quarterbacks in the game.
Inside linebacker Dannell Ellerbe continued his emergence as a leader. The pending unrestricted free agent roamed side-to-side for a team-high nine tackles.
"It wasn't easy," Ellerbe said. "Kaepernick is legit. We had to do everything we could to get him slowed down. He's the kind of guy you never completely shut down."
The Ravens needed everything they had, every defensive gambit and bit of assignment-football discipline they could harness.
In the end, Kaepernick and the Pistol offense had finally been silenced.
"It was a hard-fought game," said Reed, who was playing in his first Super Bowl as he competed in front of his family and friends from nearby St. Rose, La. "It's hard to enjoy that when you're playing a game like that against a great team. San Francisco played their hearts out. Oh, man. Oh my God. Is it real? Is it real?"