Courtois, 33, suffered an adductor injury during Madrid's goalless league draw at Rayo Vallecano on Sunday.
Madrid did not specify the estimated duration of the goalkeeper's absence, but Spanish press reports claimed he will be out for between 10 and 12 days.
Courtois could therefore be back for their league match against Elche on November 23rd.
Belgium will qualify for next year's World Cup if they win in Kazakhstan on Saturday.
They round off their Group J campaign against Liechtenstein three days later.