Matthews spoke before the game of his intentions to hit Kaepernick hard if he was given the chance, and that opportunity came when he leaped into a tackle with the quarterback running out of bounds.
The illegal hit sparked a series of scuffles between the two sides, but Matthews insists that there are no hard feelings between him and the 49ers quarterback.
"First off, it wasn't a very smart play," Matthews told The AP. "I had already committed to hitting the quarterback.
"I guess I should have figured he was going to step out of bounds. But it's nothing personal. I went up to him later and was joking around with him."
The 49ers went on to win the NFL match 34-28, with Kaepernick throwing for three touchdowns and 412 yards.