The hosts made the breakthrough in the 18th minute when Arda Turan ghosted past Adil Rami before crossing for Radamel Falcao to convert from close range.
Valencia grabbed an away goal on the stroke of half time as Jonas was on hand at the back post to tap in Rami's flick on from a corner.
Atletico were back in the lead just four minutes after the break thanks to Miranda's header following some poor defending from the visitors.
They scored again on 54 minutes when Adrian flashed a powerful drive across Diego Alves in the Valencia goal.
As the away team's defence crumbled, the home side made it 4-1 with just over 10 minutes to play courtesy of Falcao's fierce effort that flew into the top corner.
Just as Atletico looked to be crusing towards a comfortable victory, Valencia bagged what could turn out to be a vital second away goal with practically the last kick of the game through Ricardo Costa.