Mourinho's "negative" tactics in the 2-1 quarter-final first leg home loss and Pepe's stamp on Lionel Messi's hand have seen the normally supportive Madrid-based press turning on the Portuguese pair since Wednesday's game.
"I think all the criticisms aimed at Madrid, their coach and the players are very unfair," the former Real Madrid and France midfielder told sports daily As on Friday.
"Pepe is a player you almost never hear a squeak from off the pitch. He's a charming lad, very polite. But when he goes on the pitch, he is obsessed with winning and this anxiety to win sees him make mistakes.
"Obviously he has apologised for what he has done, but Pepe is a player who gives his all on the field of play, and sometimes he goes to the limit," added Zidane, who was brought in to work with Mourinho as first team director of football last July.
Madrid sports dailies As and Marca both continued their attacks on Pepe and Mourinho on Friday.
Marca questioned the club's decision to support Pepe by recording a message through their television channel on Thursday, in which he said standing on Messi's hand had been unintentional.
"Pepe has distorted reality and made Real Madrid complicit in an action which has shamed the club's fans," a Marca opinion piece said, when he "should have faced the facts and asked for forgiveness".
"NOBODY BELIEVES HIM"
A Barca vice-president Carles Vilarrubi dismissed Pepe's comments.
"Nobody believes him," said Vilarrubi, who went on to draw parallels with the incident when Mourinho jabbed a finger in the eye of Barca assistant coach Tito Vilanova at the end of the Spanish Super Cup back in August.
"The problem is that people feel protected," he told Spanish radio. "After the finger-in-the-eye incident the club issued a justification for it [when Real said Mourinho had been provoked]. This generates a culture where Pepe felt free to act and to do what he did.
"The whole world has seen it. Barca don't need to make official complaints."
Marca's leading story on Friday, titled "The seven sins of Mourinho," knocked the former Chelsea and Inter Milan coach's tactics, choice of personnel, substitutions and post-match analysis of the Cup game.
Zidane said of the attacks on Mourinho: "How can they say we need a change of coach? Are they mad or what? Look at the statistics since he has been here, they are incredible.
"To think that some doubt his commitment to Madrid and that he will stay only two years and then go. Sincerely, I would prefer that he stayed only two or three years and did something great, to someone else who stayed ten and did nothing."
Leaders Real Madrid host Athletic Bilbao in La Liga on Sunday and will then seek to overturn their King's Cup deficit in the second leg at Barcelona next Wednesday.
