Reserve keeper Antonio Adan was selected in his place as he had occurred in the 3-2 league defeat at Malaga just before the mid-season break.
Casillas's name was cheered by fans at the Bernabeu when his name was read out among the substitutes, but Mourinho's was met with whistles from sections of the crowd.
After only six minutes, with Real already leading 1-0 through Karim Benzema, Adan was sent off for a foul in the area and Casillas was brought on as a replacement to a huge cheer from home fans, though he failed to stop the ensuing penalty.
Mourinho's decision to drop Casillas, who is also captain of world and European champions Spain, has raised eyebrows though he defended his original decision as being based on 'technical reasons' in Malaga.
In Saturday's pre-match news conference the former Chelsea and Inter Milan boss spoke of the necessity for competition for places and said whoever played on Sunday would not be playing in the King's Cup on Wednesday.
(Reporting by Mark Elkington, editing by John Mehaffey)