Courtois' absence leaves manager Jose Mourinho without a key player for a vital clash with their league-leading rivals.
The 34-year-old Belgian will miss his first game this season.
Andriy Lunin is in line to replace Courtois in goal at Camp Nou.
Lunin's last appearance for Real Madrid came on May 3, in a 2-0 win over Espanyol.
Illia Voloshyn has been called up to the senior squad, with Sergio Mestre the other goalkeeper in the matchday squad.