The holders are through to the quarter-finals courtesy of two headed goals, while Dani Parejo was sent off for the visitors late on
A header from Diego Godin shortly after half-time gave Diego Simeone's men the lead, which on the balance of play was just about deserved.
Raul Garcia then sealed a 3-1 aggregate triumph when he flicked in 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, who initially looked devoid of any imagination, energy and creativity in an insipid first-half display.
However, Valencia, who made seven changes to the side that lost 2-1 to Celta Vigo, were just as lacklustre, and needed to score on the night if they harboured ambitions of reaching the quarter-finals 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 minutes, showing good close control before lashing a shot towards the target which was deflected out for a corner.
Thibaut Courtois was rarely tested but Valencia's Juan Bernat brought a comfortable save out of the Atletico goalkeeper to bring an end to a disappointing first half.
Atletico grabbed the elusive opener shortly after the break, as Godin nodded in at the back post from a teasing Gabi 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 their 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.
The hosts weathered some second-half pressure from los Che but Garcia 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 to seal a place in the last eight.