The Brazilian defender headed in a 99th-minute cross to clinch a first victory over Los Blancos since 1999 and the 10th domestic cup success in their history.
Mourinho's side had looked on course to maintain their hoodoo over their neighbours when Ronaldo powered home a 14th-minute corner.
However, Diego Costa restored parity just before half time when he fired home a 20-yard shot following a fine turn and pass from Radamel Falcao.
Real dominated but contrived to hit the woodwork on no fewer than three occasions with Mesut Ozil, Karim Benzema and Ronaldo going close to winning it in normal time.
Los Merengues then saw their evening turn sour when the referee sent Mourinho from the dugout before Miranda pounced to give Atletico the lead early in extra-time.
And Real's hopes were all-but ended when Ronaldo saw red for lashing out at Gabi.
The Rojiblancos midfielder was also sent off for a second bookable offence deep into added time but it was not enough to deny Atletico a famous triumph.
Real came into the contest hoping to maintain an imperious record against their neighbours stretching back 14 years, and they looked on course to do so when they struck first blood early on.
Ozil delivered a probing corner from the right, allowing Ronaldo to rise and direct a thumping header into the far corner.
It was the Portuguese star's 53rd goal of another remarkable season in front of goal and seemed set to be the beginning of another dominant display from Los Blancos.
However, Atletico responded and despite struggling to trouble Diego Lopez in the Real goal, they eventually made the pressure count on 35 minutes.
The effervescent Falcao twisted and turned on the halfway line before sending a sublime through ball into the path of Costa. The Brazilian took a touch and fizzed a low shot beyond Diego Lopez that crashed in off the far post for his eighth effort of this season's Copa.
The goal seemed to give Diego Simeone's side a real lift but it was Real who almost stole ahead prior to the break when Ozil pounced on a loose ball and drilled in a low shot that cannoned back off the post.
Los Blancos stepped up a level following the break and should have led on the hour mark.
First, Benzema saw his close-range shot from Ronaldo's cut back rebound back off the post, before JuanFran somehow denied Ozil with a sensational goal-line clearance.
And Real struck the woodwork for a third time soon after when Ronaldo's free-kick came back off the near post, with Michael Essien blazing the loose ball over the top.
It was all too much for Mourinho who vented his frustration at some of the referee's decisions, leading to the Real coach being sent from the bench 14 minutes from the end of normal time.
Atletico had barely threatened during a second-half onslaught but held firm to force extra-time.
And they seemed to gain a second wind from the restart, stunning the Bernabeu by snatching the lead on 99 minutes when Miranda pounced with a near post header to guide Koke's right-wing cross into the net.
Real tried desperately to fight back and Thibaut Courtois produced two sensational saves to maintain their lead as he denied both Gonzalo Higuain and Ozil with stops from point-blank range.
The frustration was etched across the faces of every Real player and their hopes were all-but ended in the second period of extra-time when Ronaldo was shown a straight red card for lashing out at Gabi.
The Spanish midfielder returned to the field with a bloody nose and also saw red in added time, but it did little to dampen the celebrations on a historic night for Atletico.
MAN OF THE MATCH
Miranda (Atletico) - A vital winner and an imperious display at the back for the Brazilian as Atletico ended a 14-year hoodoo against Real, ensuring what could be Mourinho's final season at the club ended in disappointment.
PLAYER RATINGS
REAL MADRID: Diego Lopez 6, Ramos 6, Coentrao 6, Khedira 6, Cristiano Ronaldo 7, Benzema 7, Ozil 7, Xabi Alonso 7, Essien 7, Albiol 6, Modric 6. Subs: Higuain 5, Di Maria 5, Arbeloa 5.
ATLETICO MADRID: Courtois 7 , Juanfran 7, Godin 7, Miranda 8, Filipe Luis 7, Gabi 7, Mario Suarez 7, Koke 7, Turan 7, Diego Costa 7, Falcao 7. Subs: Lopez 5, Cristian Rodriguez 5, Raul Garcia 5.
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