A hero to Real fans and a fixture between the posts for more than a decade, Casillas was a nervous spectator on the bench as number two keeper Antonio Adan conceded three times and the champions slipped 16 points behind Barcelona, 3-1 winners at Real Valladolid.
Mourinho told a post-match news conference the decision was "purely technical" and appeared to suggest that Adan had been picked because of Casillas's recent performances.
Asked whether he had relegated the Spain international to the bench because he believed Adan was the better keeper, Mourinho said: "In my opinion? Of course.
"As it's the opinion that counts, as it's the coach who chooses and as I consider the opinions of my assistants valid we decided," added the Portuguese.
"It seems to me...the work of the keeper who played had absolutely no bearing on the outcome of the game.
"The coach analyses the situation and analyses the players available, chooses the team to play.
"You can invent all the stories you like but it's a purely technical decision and nothing more."
He later said Casillas was not the only aspect of Real's game that had needed fixing.
"No it was a general problem. We haven't been playing well in different aspects of the game, one of which was our defensive work."
Sergio Ramos, another of Real's club captains, was asked in a television interview if he had been surprised by the decision to leave out his Spain team mate.
"Of course, he is usually the captain of this team and I think he will remain so as he is a great goalkeeper," Ramos said.
Adan could do little to prevent Malaga's first and third goals but was perhaps guilty of leaving his near post exposed for their second, when a first-time shot from Roque Santa Cruz squeezed past him.
Real return to action on Jan. 6 when they host Real Sociedad in La Liga. (Reporting by Iain Rogers; Editing by John Mehaffey)