In a game where chances were of plenty, it took an extra time goal from Joao Miranda to decide the where the Copa Del Rey trophy would go.
Despite their superiority in attack, the stubborn defence of Atletico held firm as they played to 1-1 draw in regulation time.
It took a goal from Joao Miranda five minutes from the end of the first half of extra time to seal the deal as Ateltico ran out 2-1 winners on the night.
It was a vastly superior display from Real Madrid, but poor decisions and hot headed tempers in the final third cost them the title.
Jose 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 then 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.
But Los Blancos 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 Spaniard was sent off for a second bookable offence deep into added time and it was t enough to hand Atletico a famous triumph.