Thomas Partey could have opened the scoring for Atletico in the fifth minute with a fantastic curling shot from the right side of the box but his effort sailed inches wide.
Sergi Darder went through clear on goal in the 14th minute and should have grabbed the lead for the hosts but Jan Oblak pulled off a point-blank range save.
Oblak produced a great reflex save to deny David Lopez in the 27th minute who hit a thunderous strike from 20-yards out.
Diego Simeone's troops could not combine effectively going forward which led to a lack of chances.
Neither side could carve out an opening in the closing stages of the half and they went into the break scoreless.
Saul Niguez had an opportunity to break the deadlock for Atletico seven minutes into the second half but his strike from the edge of the box went over the bar.
Simeone made his first change in the 65th minute by bringing on Angel Correa in place of Partey.
Atletico were probing after 70 minutes but they could not create goal-scoring chances.
With 10 minutes remaining, Gerard Moreno broke through on a counter-attack, but Oblak made a superb save to keep the visitors in the tie.
Sergio Garcia sealed the win for the hosts two minutes before time with a well struck shot from close range following a through ball from Esteban Granero.