It could have been a very different story for the home side had they enjoyed better luck in the first half, but there was a strong feeling of frustration as Gareth Bale rattled the crossbar with a free kick before Cristiano Ronaldo headed against the frame of the goal.
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After coming so close to the opening goal on two occasions, the Real supporters were left stunned as they fell behind to a goal from Paco Alcacer, who found the space to convert from an inviting Jose Luis Gaya cross.
Valencia added a second just six minutes later when Javi Fuego capitalised on some poor marking from the home defence to head in Dani Parejo's free kick.
Diego Alves was forced into action as he made a diving save from Bale's long-range strike, and the Valencia goalkeeper enjoyed a slice of luck when Javier Hernandez could only hit the post after linking up with his Welsh teammate.
Carlo Ancelotti's side were offered a route back into the match just before the interval when Gaya was adjudged to have fouled Bale while attempting to prevent the winger from connecting with a cross.
However, Alves refused to be beaten as he guessed correctly to get a strong hand to Ronaldo's penalty and protect Valencia's two-goal advantage heading into the interval.
Los Che responded well to the constant pressure which arrived early in the second half as Bale miscued a volley from close range before Alves kept out a powerful strike.
Real did manage to reduce the deficit from the corner which followed as Pepe climbed highest in the box to power a head past Alves.
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The onslaught continued as Valencia dropped deeper to protect their lead, but some stubborn defending frustrated the hosts for long spells of the second half.
James Rodriguez delivered an inch-perfect free kick into the box to create a great chance for Sergio Ramos, who became the latest victim of Alves's heroics as the Brazilian somehow managed to keep out the close-range header.
The visitors could have wrapped up the game when Alvaro Negredo fired over after being played through by Rodrigo De Paul, and the striker was guilty of wasting another chance when he headed over the crossbar moments later.
Negredo's misses proved to be crucial as Real equalised in impressive fashion when Isco cut into space before beating Alves from 25 yards.
Real were forced to commit men forward as they searched for a season-saving goal, and they were almost punished at the other end as Parejo shot over from just inside the box.
Both sides threatened to find the winner in the final minutes, but Valencia held on for the draw to leave Real four points behind Barcelona at the top of the table.