The Los Blancos skipper has been training on his own this week as he battles with a shoulder injury.
Real manager Rafa Benitez will also be without Gareth Bale, James Rodriguez and Danilo for the trip to San Mames.
Benitez's side are third on the table with 10 points from four games - two points behind pace-setting neighbours Atletico Madrid and champions Barcelona.
Bilbao are 14th in the standings with three points.
Real match-day squad:
Goalkeepers: Keylor Navas, Kiko Casilla, Ruben Yanez.
Defenders: Raphael Varane, Pepe, Nacho, Marcelo, Dani Carvajal, Alvaro Arbeloa.
Midfielders: Toni Kroos, Casemiro, Mateo Kovacic, Luka Modric, Denis Cheryshev, Isco.
Forwards: Cristiano Ronaldo, Karim Benzema, Lucas Vazquez, Jese.