After gashing the Packers' defense for one big play after another four months later, he was in the NFL record books.
Kaepernick's playoff debut for the ages propelled the 49ers to their sixth Super Bowl appearance, but he'll be a marked man as his first season as a starter begins Sunday against a visiting Packers team ready for revenge.
Alex Smith led San Francisco to a 6-2 start in 2012 that included a 30-22 Week 1 win at Lambeau, with the 49ers running for 186 yards - 17 on Kaepernick's only carry - to set the tone for a team that would finish with the NFL's fourth-best rushing offense.
But San Francisco's transformation from a defense-first team with a caretaker quarterback to a dynamic, Super Bowl contender didn't take place until Kaepernick took over under center following Smith's Week 10 concussion. The 49ers averaged 26.3 points in Kaepernick's seven regular-season starts - up from 23.6 in Smith's first eight - before finding out the entirety of what their 2011 second-round pick could bring in the postseason.
Kaepernick passed for 263 yards and ran for an NFL quarterback-record 181 yards while accounting for four total touchdowns in the 49ers' 45-31 divisional dismantling of Green Bay. San Francisco piled up a franchise postseason-record 579 total yards.
"When the quarterback can run like that, that opens up the arsenal of play-calling," defensive lineman B.J. Raji told the Packers' official website after the loss. "Obviously if you can't stop the run, that's football 101."
Kaepernick averaged 10.6 yards per rush in three postseason games and 9.98 yards per pass attempt, nearly leading the 49ers back from a 22-point third-quarter deficit before they fell 34-31 to Baltimore in Super Bowl XLVII.
Frank Gore ran for more than 110 yards and a touchdown in each matchup with the Packers last season, but the 49ers were far from the only ones who had little trouble running on them. From December on, including its two playoff games, Green Bay allowed an NFL-worst 5.81 yards per carry.
Linebacker Clay Matthews signed a five-year, $66 million extension in the offseason, and along with fellow linebacker Nick Perry - whose rookie season ended in mid-October due to a wrist injury - a Packers pass rush that finished fourth in the league with 47 sacks should be in good shape.
"We had an entire offseason to focus on last year's loss, having time to kind of figure out a way to defend (Kaepernick)," Matthews said. "We obviously like to think we're better prepared to defend that type of offense and what he brings to the table."
San Francisco coach Jim Harbaugh's biggest concern is keeping his quarterback healthy. Harbaugh went to the league for clarity about when Kaepernick is supposed to be safe before declaring himself a runner, and says he plans to talk to the officials prior to the game.
Packers coach Mike McCarthy, meanwhile, simply wants to keep Kaepernick in the pocket.
"The reality is, it is a new year, this is a different game, and we're prepared for a totally different outcome,'' McCarthy said Wednesday. "He had a heck of a night last year.''
Even if the Packers can keep Kaepernick from escaping, their secondary could have some issues. Gone is safety Charles Woodson, while cornerback Casey Hayward missed much of training camp with a hamstring injury and is uncertain for Sunday.
Green Bay's offense will look a bit different as well. Top receiver Greg Jennings signed with Minnesota and projected starting running back DuJuan Harris is out for the year with a knee injury, as is left tackle Bryan Bulaga. That means rookie David Bakhtiari will be tasked with protecting Aaron Rodgers' blind side after the 2011 MVP was sacked a league-high 51 times in 2012.
The Packers' first-team offense failed to score a touchdown in five preseason drives, but Rodgers wasn't too concerned.
"It's preseason. We had five good drives. No three-and-outs, one sack, we lost the ball on downs, missed a field goal and had three field goals," Rodgers said. "So we had productive drives. The biggest issue is we didn't have our whole team together."
Rodgers still has plenty of useful weapons with Randall Cobb, Jordy Nelson, James Jones and Jermichael Finley, but he'll have a new back behind him. Second-round pick Eddie Lacy is expected to get the start in Week 1 after running for 1,322 yards and 17 touchdowns for national champion Alabama last season.
He'll be running into one of the league's toughest defensive fronts. San Francisco allowed 94.2 rushing yards per game last season - fourth-best in the NFL - and has given up a league-low 10 rushing touchdowns over the past two seasons. That unit should be even better if All-Pro linebacker Patrick Willis, nursing a broken right hand, plays Sunday as expected.
For as much hype as Kaepernick has gotten, he'll also have to adjust without some key weapons. Michael Crabtree (Achilles) is out until at least November and Mario Manningham (ACL) won't play until at least mid-October, leaving little-used Kyle Williams as one of the 49ers' two starters at receiver.
The other, though, figures to be rather reliable alongside star tight end Vernon Davis. Just five weeks after Anquan Boldin torched San Francisco's secondary for 104 yards and a touchdown in the Super Bowl, the 49ers traded a sixth-round draft pick for the 10-year veteran.
"We do it by committee," Williams told the team's official website. "It's hard when you (don't) have a guy like Crab. He's definitely a No. 1-type of receiver. ... You could say the same thing about Anquan."
Though the pieces seem to be in place for the 49ers to contend again, they'll have to buck a major trend. No team has lost in the Super Bowl and won it the following year since the 1972 Dolphins, and none have even made it back to the Super Bowl since the 1992 Bills.