Diego Simeone's side were not at their best against their sixth-placed opponents, and were fortunate their goalkeeper was on top form - particularly in the first half
The visitors went ahead through Jonas early on, but were soon pegged back by los Rojiblancos as Radamel Falcao equalised with a neatly-taken volley shortly after.
Ernesto Valverde's team had 12 shots at goal in the first half but were thwarted on a number of occasions by some inspired goalkeeping from the on-loan Thibaut Courtois.
The odds were stacked against them as they travelled to Madrid, with Atletico having won 39 of a possible 42 points at the Calderon this season. Los Che were also without three of their first-team, including top goalscorer Roberto Soldado.
Despite their depleted squad, it was Valencia that raced into a 1-0 lead in the 5th minute when Jonas fired the ball between Courtois' legs and into the net from eight yards out. Some poor defending from Atletico allowed the Brazilian to score, as he profited from being afforded a second goalscoring chance in the space of seconds by the dawdling defensive duo of Diego Godin and Miranda.
However, their advantage lasted just 90 seconds, as Atletico quickly levelled through Falcao - a player who went in to the game having never scored against Valencia. The Colombia international raced on to a deft chipped pass from Arda Turan and slipped a neat volley past Diego Alves.
Valverde's men were not put off by Atletico's quick reply though, and they continued to push forward, particularly through Joao Pereira and Andres Guardado on the wings.
Only a fabulous save from Atletico's Courtois kept Dani Parejo's ambitious long-range free kick out in the 21st minute, while an intelligent move between Andres Guardado and Parejo was emphatically brought to an end by a perfectly-judged sliding tackle by Gabi inside the penalty area.
Two more fine stops from Courtois before the break kept the score level, as Valencia controlled the first half for long periods.
The start of the second was punctuated by some nasty challenges from players on both sides, and Atletico's Miranda spent a couple of minutes receiving treatment in the centre circle after an ill-timed tackle by Pablo Piatti.
Some smart goalkeeping from Alves stopped Diego Costa from putting Atletico ahead in the 60th minute, as the Spaniard raced from his line to push the ball away from Costa just as he prepared to shoot after taking Falcao's sumptuous looping pass in his stride.
Despite making a defensive substitution as Simeone's side started to threaten by bringing on Aly Cissokho for the quiet Nelson Valdez, los Che nearly sealed all three points when Parejo lashed a long-range strike just wide in the 85th minute.