Defensive tackle Tommy Kelly chases 49ers quarterback Colin Kaepernick during the Cardinals' 20-17 loss Sunday.

SANTA CLARA, Calif. – This was the second strike, and the Cardinals know one more could mean they're out.

For the second straight game, a mobile quarterback wreaked havoc on the defense. Last week it was Seattle's Russell Wilson who caused trouble with his arms and legs. On Sunday afternoon, it was Colin Kaepernick.

The 49ers' signal-caller was 15-of-26 for 204 yards passing with a pair of touchdowns and added seven carries for 63 yards in the 49ers' 20-17 victory. The Cardinals will face the Panthers and running quarterback Cam Newton in the wild card round next weekend, realizing if they don't keep him contained, it could end their season.

"It's going to be three weeks in a row, the same style," coach Bruce Arians said. "Hopefully we've learned from it."

Missed tackles were a big culprit against San Francisco, as the defenders had Kaepernick in their grasp countless times before he managed to wiggle free. Another issue was the lack of gap integrity, which gave Kaepernick lanes to run.

It didn't help matters to have veteran linebacker Larry Foote inactive with a knee injury. He had played nearly every defensive snap of the season previously, and while Foote was still yelling the 49ers plays from the sidelines, it wasn't nearly as impactful as having him on the field.

Linebackers Glenn Carson and Kevin Minter filled in, and while Carson finished with a game-high nine tackles and Minter was third on the team with six, they weren't thrilled with the performance. San Francisco running back Frank Gore had 25 carries for 144 yards and San Francisco finished with 206 yards on the ground.

"To go in there and play that many snaps was a good feeling," said Carson, who saw his first significant action after making the team in training camp as an undrafted rookie free agent. "At the same time, they ran the ball too much on us. As a middle linebacker, every time the ball gets run down your throat a little bit you take it as a personal responsibility."

The Panthers will follow the same formula as the two teams before them, with the mobile quarterback and a powerful running game. The Cardinals' defense knows it must answer the challenge moving forward.

"We've learned that, especially with scrambling quarterbacks – this week it's Cam Newton – we've got go get them down," linebacker Sam Acho said. "We've got to be defensively sound. It's nothing they're doing. It's us not being in our gaps. It was the same thing a couple weeks ago with Russell Wilson. From the outside looking in, the media might say, 'He's just an unbelievable quarterback.' That's not the case. They (Kaepernick, Wilson and Newton) are all good quarterbacks, but if we do our job, a good defense stops a good offense any day."

HARBAUGH OUT AS COACH OF 49ERS

Jim Harbaugh was given a game ball and Gatorade shower when the contest came to a close, as some of the 49ers showed appreciation for their now-former coach.

After months of rumors, it didn't take long afterward for the team to announce it was mutually parting ways with Harbaugh after four seasons. The 49ers finished 8-8 this season and missed the postseason. They made the NFC Championship game in each of his first three years at the helm, highlighted by a Super Bowl run following the 2012 season.

"I thought we accomplished great things," Harbaugh said. "Tremendous football, and so many people to thank for that. So many people work so hard to construct where this football team is and feel great to be part of it. (I) feel it's been the signature years in my life."

While it's widely believed Harbaugh will take the head coaching job at the University of Michigan, he declined to confirm that speculation.

"There will be announcements made concerning those things," Harbaugh said.

RUNNING GAME GETS BACK ON TRACK

Arians felt he got away from the running game too early against the Seahawks, and stayed with it consistently against the 49ers.

Running back Kerwynn Williams had only two carries for four yards last week but finished this one with 17 rushes for 67 yards. Stepfan Taylor added seven rushes for 26 yards. It helped out quarterback Ryan Lindley, most notably on an early flea-flicker in which the safeties were sucked up and he found Michael Floyd for an easy touchdown.

"We came in wanting to establish the run and be a balanced offense," Williams said. "I think we executed the run game as well as the pass game. Ryan (Lindley) had a great day."

ACHO GETS FIRST SACK OF THE SEASON

Kaepernick avoided several near-sacks, but linebacker Sam Acho was one guy who brought him down. Alex Okafor brought pressure on the play from the left, which forced Kaepernick to roll to his right and into a waiting Acho.

Acho didn't have a sack previously this season.

"It felt good, but overall we don't have a good feeling right now," Acho said. "You never have a good feeling after you lose."