Pepe was at the centre of controversy following the first leg after appearing to deliberately step on the hand of Barca forward Lionel Messi, with the Spanish press branding the Portugal international "shameful" and "embarrassing" the following day.
The 28-year-old subsequently issued an apology, insisting the act, which was missed at the time by the referee, was unintentional.
Pepe missed Sunday's Primera Division match against Athletic Bilbao through injury but Mourinho confirmed that the defender would play if fit.
Lassana Diarra and Esteban Granero were also fitness doubts but both have been named in Mourinho's 22-man squad alongside Pepe. Sami Khedira and Angel Di Maria miss out through injury.
Barca lead 2-1 from the first leg at the Bernabeu.