Mourinho and Ronaldo off as Atletico stun Real
Real had been unbeaten in the previous 25 meetings between the two rivals dating back 14 years and Mourinho's men got off to the perfect start when Cristiano Ronaldo headed in Luka Modric's corner.
However, Diego Costa levelled for Atletico 10 minutes before half-time and Los Rojiblancos then rode their luck as Mesut Ozil, Karim Benzema and Ronaldo all hit the post for Real.
Mourinho was sent from the touchline 13 minutes from normal time for taking his protestations towards the officials too far before Miranda headed Atletico in front eight minutes into extra time.
And there was even more drama to come as Ronaldo was then shown a straight red card for reacting angrily to a late challenge from Gabi with six minutes of extra time remaining.
"We had two clear chances on goal, we hit the post three times -- this is why I think it is unfair," said Mourinho.
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 Sergio 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 as Falcao called Mourinho's decision to field Albiol into question as he turned the Spanish international on halfway and then 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 from similar range.
It was Atletico though who had the clearer openings in a lively start to the second period as Filipe Luis fluffed a decent opening when he dribbled a shot into Lopez's arms and the full-back had another effort on goal moments later when he fired Gabi's cross just wide of the target.
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 Karim Benzema before Juanfran somehow blocked Ozil's follow-up effort on the line.
Real then struck the post for the third time as Ronaldo surprised the Atletico wall with a free-kick struck along the ground that came back off the upright.
Mourinho was then sent from the touchline for protesting after a number of marginal decisions went against his side.
Mourinho's message did still reach the Real bench before extra time kicked off as he made a triple substitution with Gonzalo Higuain, Angel Di Maria and Alvaro Arbeloa introduced.
However, it was Atletico who had the first great chance in extra time as Costa was released clean through on goal but this time placed his effort too close to Lopez who made a comfortable save.
From the resulting corner though 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.
Falcao nearly settled matter minutes later when a free-kick that just landed on the roof of the net, but Atleti were grateful to two incredible saves from Courtois to see them over the line.
Atletico's task in the final minutes was made far easier when Ronaldo kicked out at Gabi and saw a straight red card.
Gabi was then also shown a second yellow as both sides finished with 10 men, but Simeone's team held on to seal their third trophy in little over a year.
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