Real had been unbeaten in the previous 25 meetings between the two sides dating back 14 years and Mourinho´s men got off to the perfect start when Ronaldo headed in Luka Modric´s corner.[break]
However, Diego Costa levelled for Atletico 10 minutes before half-time and Los Rojiblancos rode their luck as Mesut Ozil, Karim Benzema and Ronaldo all hit the post for Real.
Mourinho, expected to be back in charge at Chelsea next season, was then sent from the touchline 13 minutes from the end of normal time before Miranda headed Atletico in front eight minutes into extra time.
There was even more drama to come as Ronaldo was shown a straight red card for reacting angrily to a late challenge from Gabi with six minutes remaining.
"We had two clear chances on goal, we hit the post three times -- this is why I think it is unfair," said Mourinho.
But Gabim who was also sent-off, insisted his side were worthy winners.
"This team has worked hard, to be here with the fans," Gabi told TVE.
"We deserve it, this victory is for them, for those people that have waited 14 years to see Atletico beat Madrid."
Real captain Sergio Ramos was left to rue their missed chances throughout the 120 minutes.
"After the first goal we maybe relaxed and they pushed us back," he said.
"We have four or five clear chances and when you don´t take them, then you regret it. It is clear that this is the reality and we have to accept it."
Mourinho, who could well have sat on the Real bench for the last time as he is now likely to receive a four-game touchline ban, continued to controversially freeze out Pepe after his outspoken comments against the coach.
Raul Albiol was preferred alongside Ramos in central defence.
However, buoyed by the confidence that they had won all eight derbies during Mourinho´s reign, Real took just 13 minutes to make the breakthrough as Ronaldo was given far too much room by Diego Godin and Radamel Falcao to register his 55th goal of the season with a precise header.
Gabi responded for Atletico with their first shot on goal moments later that flew over the bar, but despite enjoying a decent spell of possession, Diego Simeone´s men were finding it difficult to create a clear-cut opening.
However, when it did arrive on 35 minutes they took full advantage. Falcao called Mourinho´s decision to field Albiol into question as he turned the Spanish international and released Costa to fire in his eighth goal in the competition with a low drive past Diego Lopez.
The equaliser sparked Real into life in the final throws of the opening half as Modric drilled a low shot just wide from the edge of the area before Ozil struck the inside of the post with a half-volley.
Real ought to have been back in front on the hour mark as Ronaldo burst down the left and his cut back was fired against the post by Benzema.
Real then struck the post for the third time as a Ronaldo free-kick came back off the upright.
Mourinho was then sent from the touchline for protesting after a number of marginal decisions went against his side.
Atletico had the first chance in extra-time as Costa was released clean through on goal, but his effort was too close to Lopez.
From the resulting corner they did take their chance as Koke´s second attempt at a cross from the right was flicked in at the near post by Miranda.
Atletico´s task in the final minutes was made easier when Ronaldo kicked out at Gabi and saw a straight red card.
Gabi was also sent off but Simeone´s team held on to seal their third trophy in little over a year.
My worst ever season, says Mourinho
MADRID, May 18: Real Madrid manager Jose Mourinho described his side´s season as the worst of his trophy-laden, colourful career after Atletico Madrid edged a 2-1 extra-time Spanish Cup triumph.
Real have already surrendered their La Liga title to Barcelona and were eliminated by Borussia Dortmund in the Champions League semi-finals, leaving the former Chelsea boss to lament a return of just the Spanish Supercup in terms of silverware.
"A career is made up of many years, not just one. I don´t know anyone who always has fantastic seasons, winning important titles," said Mourinho, whose desperation was illustrated when he was sent to the stands on Friday.
"This is the worst season of my career with a title that is not sufficient to satisfy Real Madrid and therefore it is a bad season.
"With a final, a semi-final, second place in the league and the Supercup, what for many would be a good season, for me is the worst."
Mourinho, who is widely expected to be back in charge at Chelsea next season, refused to speculate on whether or not he would be in the Real hot-seat for a fourth year.
"I have a contract for three more years and I have still not sat down with the president to talk about my future," he said.
"It is normal to me that they talk about (Carlo) Ancelotti or someone else. Also that they speak about me going to Chelsea, or here or there.
"I have to be honest. Until the day that the president sits down with me and the club does something official it has to be like this."
Mourinho insisted Atletico had not been deserving winners.
After goals from Cristiano Ronaldo and Diego Costa had the scores level at 1-1 just before half-time, Real went on to hit the post three times before Miranda scored the winning goal for Atletico eight minutes into extra time.
Mourinho´s men still went on to miss two glorious chances to level through Gonzalo Higuain and Mesut Ozil before their awful night was compounded when Ronaldo saw a straight red card for reacting to a late challenge from Gabi.
"The result is 1-1 and it is not normal to hit the post three times," added Mourinho.
"You don´t have to be a magician of football to think that the result is not fair, that Atletico are not the deserved winners of the final.
"In extra-time we had two opportunities, one for Higuain and the other for Ozil. The result is not deserved, but in football everything is forgotten.
"The refereeing is forgotten, the shots off the post are forgotten, all that remains is that the winner is Atletico."
Atletico boss Diego Simeone lauded his players as they followed up their Europa League success of last season with their first Copa del Rey title in 17 years.
"It was an incredible game. We had the luck you need to have to be champions," he said.
"Then we had two chances, but what these players have done in a year and a half is incredible. I don´t have words for it."
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