The Atletico Madrid duo have lost their race against time to be fit for Tuesday's game, with the club confirming that they have been left out of the provisional matchday squad
Goalkeeper Courtois has been suffering from back spasms, while attacker Villa limped out of the 4-0 victory over Real Sociedad on February 2 with a hamstring strain.
Dani Aranzubia, who featured in Atleti's shock 2-0 reverse to Almeria on Saturday, will continue in goal on Tuesday, while Raul Garcia and Adrian are Diego Simeone's options up front as Diego Costa is suspended.
Atletico have not been beaten at home this season but face an almost insurmountable task in retaining the title which they won last year at the expense of their local rivals by overturning a 3-0 deficit from the first leg.
Atletico Madrid squad to face Real Madrid:
Goalkeepers: Aranzubia, Bono
Defenders: Godin, Alderweireld, Manquillo, Juanfran, Insua, Miranda
Midfielders: Mario Suarez, Koke, Raul Garcia, Arda Turan, Cebolla, Gabi, Diego, Sosa
Strikers: Adrian, Mesa