The buildup to the game saw a huge amount of Real Madrid fans outside of the ground to welcome their side, while sectors of the press also lent their support to a fightback, but it was all in vain.
If Fernando Torres returned a hero to Atletico on January 5th, his hero status will have only increased after his two goals which assured his side their place in the quarter-finals.
Torres opened his account after just a minute after a rapid move involving Antoine Griezmann. The Frenchman's pass left Torres with a tap in to score his first ever goal in the Bernabeu and that goal left Real Madrid needing to score twice in order to progress.
Torres was only starting because Mario Mandzukic had flu, but the striker made no mistake in beating Kaylor Navas.
Sergio Ramos drew the scores level on the night after an error from Atletico keeper Oblak, who collided with Diego Godin, left the Real Madrid central defender with a simple chance to score.
There was still plenty of time for Real to turn things around, but an error from Ramos in the first minute of the second half allowed Griezmann to again beat Navas and leave Real Madrid needing to score five on the night to qualify.
Ronaldo leveled the scores 10 minutes later thanks to a good cross from Gareth Bale, but Atletico are a side that knows how to defend in depth and limited Real Madrid's chances of overturning the score.
Pepe left the field for Rafael Varene shortly after Ronaldo's goal and may have a muscle problem which will keep him out of next Sunday's game in Getafe.