The 49ers radically changed their offense when the playoffs started.
They began using the pistol formation, and started running a play called the read-option that has been unstoppable.
Here's what the read-option looks like. Basically, the quarterback acts like he's going to hand it off, but at the last minute he can chose to run it himself if the defense is cheating in on the running back.
It looks like this if he hands it off:
And like this if he keeps it:
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It's a simple play with a simple philosophy — create a catch-22 where the quarterback runs it if the defense cheats on the running back, and the running back runs it if the defense cheats on the quarterback.
And the scariest thing about how the 49ers run it is this: They have don't have tendencies. Kaepernick will hand it off when the situation calls for a hand off, and keep it when the situation calls for him to keep it, and that makes it exponentially harder to defend against.
Take the 49ers' two playoff games as an example.
Against the Packers in the divisional round, Kaepernick kept the ball seven times on read-option plays, according to ESPN Stats & Info. He ended up with 181 rushing yards, and the 49ers scored 45 points.
But against the Falcons in the NFC title game one week later, Kaepernick handed the ball off on all 11 option plays that the 49ers ran. Atlanta clearly focused their defense on stopping him, so Kaepernick made the correct play and handed it off. Despite just 21 rushing yards from Kaepernick, San Francisco scored 28 points in the final three quarters.
That's the beauty of the read-option — if the defense takes away one option, the other option becomes that much more potent.
San Francisco's option play isn't so good just because they have a great running back (Frank Gore), and a great running quarterback (Kaepernick). It's so good because the defense truly doesn't know where the ball is going.