Pepe has been frozen out since criticising Mourinho last weekend.
"It was my decision and that’s it. I'm the coach. I don’t have to justify anything," said Mourinho.
"From the first to the last day I'll always be the one to decide. Sometimes I can share the reasons for my decisions and sometimes not, I'll take that option. On Friday you'll see who plays and it will always be my decision and responsibility."