Taking advantage of creases largely caused by the Falcons' determination not to let Kaepernick get outside, running backs Frank Gore and LaMichael James rushed for 124 yards and three touchdowns, and tight end Vernon Davis, who had caught just seven passes in the Niners' previous seven games, had five catches for 106 yards and a touchdown.
Kaepernick completed 16 of 21 passes for 233 yards.
On Sunday, yet another team, the Baltimore Ravens, will try to take Kaepernick's legs out of the equation, while at the same time do a better job than the Falcons of neutralizing him as a passer and keeping Gore and James in check.
"We're going to have to tackle him," Ravens coach John Harbaugh said. "We're going to have to keep him inside and in front of our defense. We're not going to be able to run past him.
"He's fully capable of putting 200 yards on you in a second, just as capable as Gore is, or any of their running backs. He's not just an integral part of their passing game, he's a huge part of their run game. So we'll have to plan for that. Assignment football is going to be really important for us. Changeups are going to be important for us. We'll just have to play well against it."
The Ravens have the benefit of having not one, but two, mobile quarterbacks on their team who can simulate Kaepernick in practice - backup Tyrod Taylor and practice-squad player Dennis Dixon, a former Chip Kelly acolyte at Oregon.
"They're having fun being him," Ravens defensive coordinator Dean Pees said. "It's a fun offense to run. But it's not a very fun offense to play against."
The Ravens have faced two quarterbacks this season with a similar skill set to Kapernick's - the Eagles' Michael Vick and the Redskins' Robert Griffin III. They lost to both of them.
Vick and the Eagles beat them in the second week of the season, 24-23. The Ravens did a just-OK job of containing Vick's running, holding him to 36 yards on eight carries, not including two game-ending kneel-downs. While Vick turned the ball over three times, he also completed nearly 72 percent of his attempts and threw for 371 yards.
The Ravens lost to RGIII and the Redskins in overtime in Week 14, 31-28. Griffin ran for 34 yards on seven carries and completed 15 of 26 passes for 242 yards. Like Gore and James last week, Redskins running back Alfred Morris took advantage of the attention the Ravens gave Griffin and rushed for 129 yards and a touchdown.
Asked how much his defense is going to draw on their experiences against Vick and Griffin against Kaepernick, Pees said, "Hopefully a lot. And try to eliminate some of the negative things that we did in both of those games.
"[Kaepernick] probably is a good analogy. He is probably a good combination of both of those guys in some ways. He's not exactly like either one of them, but he has traits that are similar to both. Certainly, we have looked at both of those games."
While Kaepernick may have a similar skill set to Vick and Griffin, the offense the Niners run is different than the ones in Philadelphia and Washington.
The Eagles seldom ran the read-option. Most of Vick's rushing yards came on pass plays that broke down for one reason or another.
While the Redskins run the read-option offense, they have a different blocking scheme than the Niners and run more of a veer-option, with a running back on the outside for Griffin to pitch to.
Ravens safety Ed Reed said he's been watching tapes of Vick when he was with the Falcons to help him prepare for Kaepernick this week.
"I was watching the tape of [Vick] and talking to [linebacker Ray Lewis] about him," Reed said. "I remember the days when we played against Vick and just how he can throw the ball and run. RGIII is a little bit different. Their blocking scheme, with how [coach Mike] Shanahan does things [is different than] what they're doing with Kaepernick.
"It's read-option, but there's no pitch guy, so it's a little different. To tell you the truth, I really haven't looked at our Washington film again. Even [Kaepernick's] running style - I know he's fast and he can run - but RGIII was a little quicker, I think, and a little faster. You're getting some of the same things, but not totally."
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