Antonio Conte confirmed Courtois was suffering from a "muscular problem" ahead of last weekend's FA Cup quarter-final win over Leicester City, although understudy Willy Caballero usually starts domestic cup games.
Courtois joined up with Roberto Martinez's national side but Belgium have confirmed he will continue his rehabilitation with the reigning Premier League champions and play no part in Tuesday's friendly.
"Thibaut Courtois has not recovered from his hamstring injury and left the group," read a statement issued on the team's official Twitter page.
"Roberto Martinez will decide later on who will replace him in goal versus Saudi Arabia. Get well soon, Thibaut."
Liverpool's Simon Mignolet is favourite to start in Courtois' absence, with uncapped duo Koen Casteels and Matz Sels the other goalkeepers in Martinez's squad.
Chelsea's clash with Spurs is a pivotal fixture in the battle for Champions League qualification, as Conte's men sit five points behind their fourth-placed London rivals in fifth with eight Premier League games remaining this season.