Zinedine Zidane has left the Portugal star out of his plans after he picked up an ankle injury in the 2-2 draw with Barcelona last Sunday.
It is still hoped Ronaldo will be fit for the Champions League final, though, with Zidane having backed the 33-year-old to be at "150%" for the clash against Liverpool.
Keylor Navas, Marcelo, Raphael Varane, Luka Modric and Toni Kroos have also all been rested for the trip to the Ramon Sanchez Pizjuan.
Injured duo Isco and Dani Carvajal have not been risked, while Gareth Bale, who scored the equaliser in the Clasico draw, is suspended.
Madrid play three more league games before taking on the Reds in the Champions League final in Kiev on May 26.