Mourinho took responsibility for mistakes in the team set-up and, despite insisting they were not the only poor performers, suggested the duo could have come off sooner.
"I didn't change after 20 minutes because I don't want to destroy the players," he said.
"I didn't want to make three changes at half-time because I was afraid in long 45 minutes something happened.
"If it was a sport with a free number of changes and where the changes during the first half is something normal like basketball and all this kind of stuff, I would do after 20 minutes.
"But I did at half-time, we changed the direction of the game but we didn't get the compensation I think we deserved in the second half."