That was a sound decision. The problem was that having to reset the play took away the original call, which judging by what happened just as the whistle blew was a designed run by Kaepernick.
He may have scored; who knows? The fact is, Kaepernick threw two more incompletions after the timeout, including the fourth-down attempt that left Harbaugh convinced Baltimore cornerback Jimmy Smith deserved a penalty for defensive holding.
In any case, while Kaepernick could not deliver a Super Bowl victory in the tradition of 49ers legends Joe Montana and Steve Young, he played well enough to win although he disputes that theory. "We lost," he said, "so obviously it wasn't enough."
With help from running back Frank Gore, Kaepernick came close to completing an 80-yard drive that could have overtaken the Ravens at the end, even after the 49ers trailed 28-6 early in the third quarter.
"We thought it was our game," he said.
Almost. Kaepernick's offense produced 29 points (not counting the Ravens' intentional safety), and he personally was responsible for 364 yards. Even the interception he threw in the second quarter was not harmful because the 49ers stopped a subsequent fake-field goal play.
We'll never know if Alex Smith would have won this Super Bowl, or even could have taken the 49ers to this stage. What's clear is that Kaepernick has risen to the level of a highly capable NFL quarterback, and the 49ers should have some staying power.
Already anticipating Kaepernick's further development in his third pro season, pregame.com lists the 49ers' championship odds at 8-1, even with Denver and just behind New England (7-1). Then come Green Bay at 10-1 and Baltimore and Houston at 14-1.
That's how favorably Kaepernick is perceived. And the NFL's defenses will be dealing with him for a long time to come.
"There was nothing extreme that we were doing," the Ravens' Paul Kruger said about the approach to Kaepernick. "We didn't change our whole scheme, but we knew he was going to be somebody we have to contain. We lost it a few times and he got out and hurt us with his feet, but we just had to respond to that and make sure it was always something we kept an eye on."
Kaepernick broke Young's Super Bowl record for quarterbacks with 62 yards rushing besides passing for 302 yards on only 16 completions.
He just needed to cover 5 more yards somehow. Even if San Francisco had scored a touchdown, a Baltimore field goal could have won or tied the game pending the outcome of the 49ers' two-point try. But the 49ers always will wonder what would have happened if a penalty on Smith had given them another first-and-goal opportunity.
Personally, I'd like to know whether Kaepernick would have scored on his third-down run if he had made sure the ball was snapped on time. As it was, the 49ers advanced one game beyond where Smith took them last season, but not far enough to satisfy them.
"We'll be back," Kaepernick said.