Already leading 2-1 from the first leg, Atletico overcame Segunda B outfit Reus Deportiu 1-0 at the Vicente Calderon thanks to a volley from Thomas Partey shortly after the restart.
As the tie drew to a close there was a chance for Fernando Torres to score his 100th goal in Atletico colours, but the frontman shot wide when well placed.
Elsewhere, Roberto Soldado was on target and also missed a penalty in Villarreal's 2-0 win over Huesca, which sealed a 4-3 aggregate win for the Yellow Submarine.
Manuel Trigueros put the hosts in front at El Madrigal, before Soldado failed to convert from the spot. Yet, the former Spurs frontman made amends 12 minutes from time to secure his side's progression.