Cristiano Ronaldo added to his phenomenal tally of goals this season with a 23rd minute strike to help set up a semi-final over two legs against holders Sevilla after the Andalusian club saw off Villarreal on Tuesday.
Passions ran high on a chilly night at the heavily-policed stadium in the south west of the Spanish capital and the Atletico supporters aimed ugly chants at Real coach Jose Mourinho and some of his players.
The visitors, who have not won Spain's domestic cup since 1993, had an early scare when Iker Casillas was caught in possession by Jose Antonio Reyes, who blocked the Spain goalkeeper's attempted clearance but could not make the most of the rebound.
The home side were then rocked by a double blow.
Sergio Ramos was given too much space on the right and Ronaldo powered into the penalty-area to smash a deflected cross high into the net.
It was the Portuguese forward's 32nd goal of the season in all competitions and followed up on his strike in the 3-1 win in last week's first leg at the Bernabeu.
Reyes then had to leave the pitch due to an ankle injury he had sustained in an earlier tangle with Alvaro Arbeloa and the former Arsenal winger, who also had a stint with Real, was replaced by Diego Costa.
RARELY TROUBLED
The Brazilian striker nearly created an equaliser with his first foray, cutting inside from the right and sending over a low cross that just evaded Diego Forlan.
A toothless Atletico, missing injured Argentina forward Sergio Aguero, rarely troubled Casillas in the second half and their elimination effectively ends the Europa League champions' hopes of silverware this season.
"We didn't have any problem tonight," Mourinho said at a news conference.
"We won the tie without having to run much. We were compact in defence and we knew from the start they weren't going to get many chances."
The other semi-final is between 2009 winners Barcelona and Almeria, the Andalusian club who made it through to the last four for the first time by knocking out Deportivo La Coruna on Wednesday.
A depleted Barca lost 3-1 at second-division Real Betis on Wednesday but went through 6-3 on aggregate.
The first leg of the semi-finals is next week and the return leg the following week.
