Miranda`s goal in the 99th minute was enough for los Rojiblancos to clinch their 10th Copa crown and, in the process, end their long 25-match winless run in the Madrid derby.
Cristiano Ronaldo opened the scoring just before the quarter-hour mark with a thumping header, but an outstanding combination between Radamel Falcao and Diego Costa saw the latter level the scores after 35 minutes.
Los Blancos hit the woodwork three times in their search for a winner, which proved fruitless throughout regulation time before Miranda nodded home in extra-time to send the trophy to the red half of the Spanish capital.
But there were ugly scenes towards the end, as Ronaldo was sent off in the 114th minute for lashing out at Gabi, sparking a bench-clearing clash between both sets of players and staff, before the latter also saw red for a second yellow card in the dying seconds.
Mourinho sent a clear message to Pepe by excluding the defender from his matchday squad despite Raphael Varane’s injury, instead turning to Raul Albiol to partner Sergio Ramos at the back.
Diego Simeone’s XI virtually picked itself, with Mario Suarez, recovered from a back problem, the main change, replacing Tiago in midfield.
It did not take the hosts long to strike as Ronaldo, in his 100th Bernabeu outing, powered them into the lead with 14 minutes on the clock, rising above Diego Godin to head home with authority from Mesut Ozil`s corner.
But the goal did little to spark the match into life, as both sides` defensive organization contributed to a rather cautious opening half-hour, despite a torrent of noise raining down from the stands.
However, that script was thrown out the window 10 minutes before half-time when, out of nowhere, a magnificent counterattack from Atletico carved Madrid completely in two.
Falcao did brilliantly to shake off a pair of challenges near the halfway line and release Costa, who never broke stride, streaming past Ramos and Michael Essien and drilling into the bottom corner via the post and the hand of Diego Lopez.
The game was well and truly on, with the crowd thrown into a real frenzy after the goal. And Ozil nearly blew the roof off the Bernabeu three minutes before half-time, when his snap shot cannoned agonizingly off the woodwork.
The raucous atmosphere continued into the second half, and Atletico nearly stormed into the lead on the hour mark when Gabi’s searching pass was met on the volley by Filipe Luis, but he could only find the side netting.
But Madrid were down at the other end almost instantly, and were cursing their luck after Karim Benzema poked against the post from close range, before an outrageous block from Juanfran denied Ozil’s goalbound follow up.
Fortune continued to smile on the visitors, as six minutes later, Ronaldo fooled the wall with a low free-kick, only to see his attempt bounce off the base of the post.
Tempers began to flare as the referee was forced to dish out a series of yellow cards to both sets of players – with Ramos` booking particularly riling Mourinho, who was sent from the dugout for remonstrating with the officials.
But there was nothing separating the sides as time ticked away, and the final moved into an additional half-hour for the second time in three seasons.
Mourinho wasted no time in using all three of his available subs, bringing Gonzalo Higuain, Alvaro Arbeloa and Angel Di Maria into the fray, with Benzema, Luka Modric and Fabio Coentrao departing.
But it was Atletico who nearly struck first in extra time, as Costa was released on goal, but failed to beat Lopez with his initial shot and then from the rebound.
Miranda would make no such mistake though, staying forward from a corner and rising highest to head in Koke`s cross at the near post.
Thibaut Courtois then stuck out a leg to deny Higuain from point blank range, and produced an even better save in the 109th minute, tipping away Ozil`s far-post finish at full stretch.
But it just was not Madrid`s night, as Ronaldo was shown red with six minutes remaining for a petulant reaction on Gabi, initiating a commotion between both teams, and effectively ending the home side`s chances once and for all.
Although Gabi was dismissed in the dying seconds for picking up a second yellow card, the mood amongst the legions of fans in red and white inside the Bernabeu could not be dampened, as Simeone`s side ended a 14-year curse against their rivals and lifted the Copa in the process.
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