Atletico - the cup holders - had won twice in a row in north Madrid to sorely irritate their more successful neighbours, and Carlo Ancelotti's men used Wednesday night's first-leg semi-final to convincingly reassert their authority.
Cristiano Ronaldo would not score on his 29th birthday, while Gareth Bale was absent from the squad for unspecified reasons, but an own-goal from Emiliano Insua and second-half efforts from Jese and Angel Di Maria gave Atletico a mountain to climb in next week's reverse at the Vicente Calderon.
The opening goal arrived in bizarre circumstances in the 17th minute. When Real's forwards were pushed out to the fringes of the box, Pepe picked up the ball and drove it fiercely but errantly towards goal.
His shot would have been wildly off-target but took a huge, fateful deflection off Insua to unsight Thibaut Courtois and veer into the back of the net.
Pepe risked earning an early red card for engaging in niggling challenges with Atletico's 20-goal striker Diego Costa, whose ongoing frustration with the defender took his focus off leading the visitors' line.
Away from the scrapping Real were pushing hard for a second goal and found Courtois an immovable object as the young Belgian parried shots from both Jese and Luka Modric around the half-hour mark.
Jese would have better luck after the break, the Spain Under-21 striker doubling Real's advantage shortly before the hour was up.
Di Maria provided the pass for Jese to run onto and he took the ball in his stride before beating Courtois with a low shot.
If things were starting to look grim enough for Atletico at that point, they would get worse.
Firstly, Costa earned the yellow card that ruled him out of the return leg and, in the 74th minute, Real scored their third goal.
Provider turned goalscorer as Di Maria took aim from just outside the area. Joao Miranda put his body in the way but he could not stop the ball from beating Courtois to compound a miserable night for Atletico.