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.
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.
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."
