Kaepernick threw for 158 yards and one touchdown and also ran for 138 yards, but threw two costly interceptions, including one to Richard Sherman that ended his side's chances of completing a late comeback.
Harbaugh told reporters: "I thought Colin played his ass off.
"We played well. The game itself was one of the best games I've ever witnessed as a coach or player because the players played their ass off. It was a credit to the players in the game, the way they played."
The 49ers crashed out of the playoffs in the NFC championship game for the second time in three years.