The Frenchman snapped: "In the play of the third goal, I looked to clear the ball and I felt in my back the elbow of somebody. It is clear that Raul had something to do with that play. I protested a lot because everybody saw it except the referee and his assistants.
"Madrid will be good champions, but it does not need to play with 12. Both teams played a good game."
Villarreal president Fernando Roig, however, refused to attack the match officials over Real's controversial winner.
He said: "I have seen the third goal of Madrid, but I always trust the good will of the referee because at times he can harm you and others favor you. I congratulate Madrid. With a nine point advantage, it is very difficult to see them losing the title from here."