A tight opening period was decided by just the one goal as Karim Benzema pounced in the Valencia box to thump his effort into the bottom corner.
However, it was a case of too little too late with Jose Mourinho's side advancing to the semi-finals courtesy of a 3-1 aggregate score.
There was to be late drama, however, with Angel di Maria receiving a red card as Madrid ended the match with nine men.
Here, Sports Mole dissects the 90 minutes of action between the two sides.
Was the result fair?
Taking this match as an individual result, a draw was just about fair. Valencia were the better side in the first period and perhaps should have led at the interval, but they fell behind through a strike from Benzema. In many ways, Madrid played the perfect away match this evening as they sat back and attacked on the counter. It was always going to be difficult for Valencia to turn things around from the first leg.
The Valencia supporters will not have too many complaints about their team's performance this evening. They dominated possession for large periods against the Spanish champions, but without Roberto Soldado did not really have a player capable of taking an opportunity in the penalty area. They have been eliminated, but their performance will have boosted them ahead of the second part of the league season.
Real Madrid's performance
Madrid have certainly struggled at times this season, but they appear to be back to their best. It was a different performance from their 5-0 victory at the weekend, but it was equally as effective. They were without first-choice central defenders Sergio Ramos and Pepe, but those that took their place performed admirably. It could yet be a successful season with the Copa del Rey and Champions League to strive for.
Sports Mole's man of the match
Raphael Varane: The 19-year-old was the shining light in the Madrid defence this evening. The Frenchman showed maturity beyond his years as he dominated in the air in addition to demonstrating his fine ability on the ground. He is going to become one of the very best.
Biggest gaffe of the match
Ricardo Costa had a steady evening, but his mistake which led to the Madrid goal ultimately cost his team. A fine pass from Xabi Alonso found Benzema, but the defender failed to remain tight to the Frenchman as the striker turned and found the bottom corner.
Miguel Perez had a fairly inconsistent 90 minutes of action. The Spaniard was too picky in the opening stages, but recovered well as the match became an end-to-end affair. Meanwhile, he rightly issued two red cards to Madrid players. Neither side will have had too many complaints about his performance despite the odd grumble.
Valencia: Valencia will attempt to continue their impressive form in La Liga when they travel to Deportivo La Coruna on Saturday.
Real Madrid: Madrid also return to league action this weekend with a fixture at home to Getafe on Sunday.