Real had Raul Albiol sent off for a professional foul in the incident which led to Lionel Messi giving Barca the lead from the spot. But Mourinho insists that Dani Alves should have joined him for a similar offence which presented Cristiano Ronaldo with the chance to nick a point with a penalty of his own.
"I don't understand the reason why Dani Alves hasn't seen a second yellow after conceding a foul in the area for a penalty,'' said Mourinho. "I asked the fourth official why there wasn't a second yellow and he told me 'it's because he's a full-back'.
"When everyone thought they could destroy us playing with one player more, for 45 minutes the team was strong enough to compete and strong enough to get a result, and if the referee gives, as he should have done, a second yellow card to Alves, the last 10 minutes playing 10 against 10, it could have been a different story.
"We played very well with 10 players. We played with a lot of dignity and character and with the fans absolutely fantastic, and we almost won.
"In my opinion it was a very even game when it was 11 against 11. In the first half the teams respected each other, knowing they were facing strong opponents. There weren't many great chances, some for them some for us, but not many.
"Afterwards, with 11 versus 10, it was practically mission impossible. It would be mission impossible for many teams, especially against a side who are the best in the world at keeping possession. But once again we've been left with 10 men, a lot of time with 10 men, and once again there's been an absolutely incredible difference of criteria. I'm a little tired of playing against Barca with 10 players."
Mourinho refused to answer questions from certain members of the Spanish media following Friday's press walk-out. Scores of journalists, mainly from the local press, left the room at the club's Valdebebas training ground just prior to Friday's pre-match press conference after Mourinho's assistant Aitor Karanka was sent out to field questions in place of the Portuguese.
Dani Alves has protested his innocence over the late penalty. Alves felt the referee had got it wrong though, saying: "I don't agree with the referee's decision because I got the ball cleanly and didn't touch him (Marcelo).
"It's positive that they didn't beat us. We have to continue along this line, picking up points and trying to keep our advantage until the end. We are in the same position, but now with a game less.
"We have to continue like that because on Wednesday we have a massively important game. Let's see if we have more luck. We are very motivated for the cup, especially after this game. We deserved more and football always offers you a new opportunity and that will be on Wednesday.''
His team-mate Seydou Keita, whose side also felt they should have been awarded a penalty themselves in the first half when David Villa appeared to be brought down by Iker Casillas, added: "It wasn't a penalty. He (Alves) got the ball and it was never a foul. We don't like to talk about the referees and it's better to focus on the next matches.''
Barca coach Pep Guardiola insists there is still work to do though, saying: "We're still not champions with 18 points to play for against teams who are playing for their lives. We're happy. To come here and not lose is a good result. Madrid are a top team.''
With regards to what he can build on ahead of the cup final, Guardiola added: "You always learn something for the next game, we are going to learn how to attack them better and how to control their counter-attacks better. But it's a final and millions of situations can happen.''
Real defender Sergio Ramos insists his side will not give up their fight for the title.
"Whilst no team has been mathematically crowned champions we are obliged to carry on and put Barcelona under pressure,'' he said.