Courtois left the Ciudad Deportiva de Valdebebas early before today's training session due to gastroenteritis and is not expected to travel with the team to Athens.
Real management confirmed his absence, but left the door open to the possibility of a last-minute recovery.
They said in a statement: "Following today's assessments by our medical services, Courtois has been diagnosed with a gastrointestinal viral infection. The situation remains to be evaluated."
Courtois is now set to miss his first game of the season due to the illness.
Andriy Lunin will now step up in his place, supported by Fran González as second goalkeeper and youngster Javi Navarro, as Sergio Mestre is not included in Real's UEFA squad list.
