The Portuguese netted twice from the spot to avenge last year's Copa final defeat to Diego Simeone's men and book a place in the final against Real Sociedad or Barcelona.Two Cristiano Ronaldo penalties helped seal Real Madrid's place in the Copa del Rey final and avenge last year's defeat to Atletico Madrid.
The Portugal international's seventh-minute opener made life almost impossible for the hosts before he completed his double just nine minutes later with another spot kick to hand the visitors a dream start to the second leg.
Ronaldo was unable to complete his hat trick, however, as the 18-time winners booked a final clash with either Barcelona or Real Sociedad thanks to a 5-0 aggregate win.
Real also created a little slice of history by becoming the only team to reach the Copa del Rey final without conceding a goal.
Raphael Varane made his first start since November after suffering a knee injury, while Atletico was without key men such as Thibaut Courtois, David Villa and Tiago because of injury, with Diego Costa suspended.
Gareth Bale threatened first, glancing a header wide from Xabi Alonso's delivery, before Ronaldo was brought down in the area by Javier Manquillo after leaving Miranda for dead with an electric turn of pace.
The Portuguese stepped up to fire home the first away goal of the tie to the right of Daniel Aranzubia and register his 33rd goal of the season in all competitions.
Raul Garcia struck Real's post with an impressive long-range effort five minutes later, but Diego Simeone's men were hit with another blow when Bale was fouled by Emiliano Insua in the area.
Referee Alberto Undiano again pointed to the spot and Ronaldo firmly placed the ball in the same corner as before to double Real's advantage in the game after just 16 minutes.
Despite conceding two early goals, Atletico continued to pass the ball well, but struggled to create any real chances.
The home side's best spell came in the final 10 minutes of the half when Garcia almost found himself through on goal, only for Varane to clear, before Cristian Rodriguez fired over from the left-hand edge of the box.
Ronaldo almost completed his hat trick five minutes before the break, but screwed an effort high and wide from inside the area, before he was involved in a mid-air tangle with Manquillo.
The defender landed awkwardly on his neck but continued for the remainder of the half, with Ronaldo hit by an object that appeared to be thrown from the crowd as he left the field at halftime.
Opportunities were limited in the early parts of the second half, with Bale's dipping free kick causing Aranzubia problems 25 minutes from time.
Atletico continued to look neat in possession but failed to get behind Real other than when Jose Sosa rifled an effort at Iker Casillas, forcing the Spaniard into a smart save.
Defeat represents a third straight loss for Atletico without finding the net, with the sides set to renew rivalries in La Liga in March.