But Atlanta's performance this season in games against fast, mobile, quarterbacks indicates their defense could be in for a testing time in Sunday's battle for a Super Bowl berth.
Kaepernick set a record for the most rushing yards by a quarterback in any game with 181 yards on 16 carries with two touchdowns in Saturday's 45-31 win over the Green Bay Packers. He also threw for 263 yards and two touchdowns.
It was a performance which amply justified 49ers head coach Jim Harbaugh's decision to stick with Kaepernick even after incumbent and former top draft pick Alex Smith was cleared to return from a concussion last November.
It was also a display which will have been painstakingly examined by the Falcons defensive coaching staff this week.
"He is very impressive, he is long and he can take up a lot of ground when he is in the open, running. It is going to be important to be disciplined in our defensive assignments when you are facing that type of offense," said Smith.
The Falcons head coach has noted a very quick evolution in the second-year quarterback's play since he stepped in for the injured Smith midway through the regular season.
"He is going through a maturation process and I think their offensive staff have done a very good job at playing to his strengths and you can see each week that they are adding more to his repertoire," said Smith.
"He has done a very good job and if you don't account for him in the run game, you can see what happens. The example is last week."
Smith says his gameplan for facing the 49ers 'read option' offense has been helped by the fact that Atlanta have had plenty of experience against quarterbacks who are comfortable outside of the pocket.
"We have some familiarity with the read scheme playing twice against the Carolina Panthers and the Washington Redskins and Seattle last week. So there is some familiarity but there are a lot of nuances in what San Francisco does," he said.
The closest style to what the Falcons can expect from Kaepernick came from the Panthers and their second-year quarterback Cam Newton, says Smith.
"I think he is probably closer to Cam Newton, due to his size and stature, he is a big tall guy and once he gets going he is hard to catch," said the Falcons coach.
"When he starts to stride out, I think you can see, he can run away from defenders."
Newton, though, stands as a warning to Atlanta of what can happen if they do not figure out how to handle the 49ers' mobile quarterback.
In Week Four of the regular season, Atlanta beat visiting Carolina 30-28 in a game where Newton had nine carries and accounted for 86 of his team's 199 rushing yards, scoring one touchdown while passing for 215 yards and two scores.
In Week 14, it got worse for Atlanta as Newton had a career-high 116 rushing yards, including a 72-yard touchdown run, while throwing for 287 yards and two touchdowns in a 30-20 upset win for Carolina at home.
Last week, quick-footed Seattle Seahawks rookie quarterback Russell Wilson was the team's top rusher with 60 yards and a touchdown in the divisional playoff loss at Atlanta.
"Russell Wilson was the best example we can get for this week as far as facing Colin," said Falcons safety William Moore. "I think it prepared us a lot for this week.
"We will be focused on keeping the quarterback in the pocket."
Atlanta linebacker Mike Peterson said that the 25-year-old Kaepernick's inexperience could be a factor that works in top-seeded Atlanta's favour as they mix up the plays against him.
"He is doing a lot of great things for his team but he's still a young quarterback. He can't run from everything," said Peterson.