Three times at critical junctures, Kaepernick used his long strides to make big runs that set up scores in the visiting Niners' 23-20 victory over the Green Bay Packers in a wild-card round playoff game at frigid Lambeau Field.
"He answers in the clutch time of the game, in the important down, when it matters most," said Harbaugh. "He's Kaepernick tough. It's pretty awesome."
The long-striding Wisconsin native dashed 42 yards up the middle to help put the Niners back in front 13-7 in the first half, and after San Francisco fell back 17-13, he ripped off a 24-yard run to set up another score for a 20-17 lead.
After Green Bay tied the score 20-20, Kaepernick did it again.
On a third-and-eight from the Green Bay 38-yard line, just outside field goal range with 70 seconds left, Kaepernick rolled left to avert the rush and gained 11 yards to keep the drive alive and move the ball into game-winning field goal range.
He also gained 98 yards on seven runs, to lead the game in rushing.
Harbaugh said none of the plays was drawn up and that the close guarding of receivers by Green Bay defenders dictated the reaction of the 6-foot-5 (1.96 m) Kaepernick.
"There wasn't a whole lot called out there today," Harbaugh said about the officials giving defenders a fair amount of leeway. "Our receivers were getting grabbed. And I think Colin saw that and just took matters into his own hands."
What impressed Harbaugh most was how fast Kaepernick could turn the corner as he raced away from would-be tacklers.
"He was around the edge a couple of those times so fast, it was 15, 20 yards. It was unbelievable the way he was getting the edge. It was so clutch," the coach gushed.
"Colin Kaepernick, I think we can all agree, is a clutch performer. It's not his first time doing this."
Harbaugh drew some heat last year when he tabbed Kaepernick as his quarterback in midseason ahead of former overall number one pick Alex Smith and rode the young signal caller all the way to the Super Bowl before falling to the Baltimore Ravens.
Kaepernick, who grew up rooting for the Packers, has enjoyed some spectacular games against Green Bay.
In last year's 45-31 win in the second round of the playoffs, Kaepernick rushed for an NFL quarterback's record 181 yards with two touchdowns.
In this season's opener against Green Bay, Kaepernick set a personal best by throwing for 412 passing yards, including three touchdowns, in a 34-28 Niners' win.
Harbaugh said the way Kaepernick eats up yards with his long strides set him apart from other quarterbacks.
"The unique part is just how much ground he covers with the strides, just how fast he gets an edge," the coach said.
"How much ground he covers when he steps up into the pocket - it's five, 10, 20 (yards). It's happening pretty fast. I think that's unique. I've never seen that before."
Harbaugh passed along some praise for rival quarterback Aaron Rodgers, Green Bay's Super Bowl most valuable player three years ago, who made some crucial escapes from pass rushes to make big plays for the Packers.
"The first one that led to the touchdown was spectacular, the second one was a heckuva play as well," Harbaugh said about Rodgers' performance.
"Our quarterback had two and some more."
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