The Frenchman struck twice in the first period at the Bernabeu, but a Lionel Messi hat-trick helped the current champions claim all the points.
"We are disappointed with the result," Benzema told reporters.
"We scored three goals and had control of the game. When Barcelona don't have the ball it makes it difficult for them to have a good game.
"Barca always have possession and against a team like that we adapted our game to go forward. I scored two goals but they don't mean anything now. What matters is the result."