Pepe was sent off after Thomas Muller exaggerated their head clash.
But Mourinho told Yahoo: "'I think obviously the second goal is his fault. He's on a zone but he has to make contact with the opponents and he left Hummels and Sami [Khedira] completely on his own and nobody contacted him, no challenge and Hummels scored the second goal.
"After that I think the frustration of the mistake comes up and after that loses possession with the pressure of Muller and after that we can say is not a real aggression.
"Maybe he doesn't deserve a direct red card but because, in spite of not being a clear aggression, there is a body language that many, many times pushes the referees to have these kind of decisions.
"To leave a team playing with ten men for such a long time is obviously a big handicap for the team.
"The fact that is not even a Portuguese man, I think that should put even more pressure on him to behave in a certain way, which he didn't."
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