The holders are through to the quarterfinals courtesy of the defender and attacker's headers, while Dani Parejo was sent off for the visitors late on
A header from Diego Godin shortly after halftime gave Diego Simeone's men the lead, which on the balance of play was just about deserved.
Raul Garcia then confirmed Los Rojiblancos' place in the last eight when he flicked a header on following more suspect defending from the visitors, whose night was summed up when Dani Parejo was sent off for a second yellow at the end.
The exertion of Saturday's night clash against Barcelona had seemingly taken its toll on Atletico, which initially looked devoid of any imagination, energy and creativity in an insipid first-half display.
However, Valencia, which made seven changes to the side that lost 2-1 to Celta Vigo, was just as lackluster, and needed to score on the night following a 1-1 draw at Mestalla in the first leg.
Both sides were reduced to speculative efforts from long range to begin with in a match that rarely threatened to spring into life. Diego Costa came closest for the hosts in the opening 45, showing good close control before lashing a shot towards the target which was deflected for a corner.
Atletico grabbed the elusive opener shortly after the break, as Godin nodded in at the back post from a teasing corner.
Valencia complained that the set-piece should not have been given in the first place but the Atleti defender took full advantage of some dismal defending to score.
Atletico nearly doubled the lead a few minutes later as Jose Sosa played in an early ball into the path of Garcia, who hit a swerving shot that cannoned off the post.
But the attacker was not to be denied, as late on he scored the clincher, flicking on at the near post beyond the helpless Guaita in the Valencia goal.