After their resounding 4-0 first-leg win coach Diego Simeone used his squad players to finish off the contest at the Calderon but it was the third division side who scored first through Alberto Corroza.
The defender was quickest to react when an Adrian Mourino free kick was turned on to the post by Daniel Aranzubia and he slotted the ball home after 14 minutes.
Atletico had a golden chance to equalise when Adrian Lopez was fouled by keeper Jose Miguel Morales for a penalty but Adrian blazed his spot-kick over the bar.
Adrian, however, made amends 12 minutes from the end when he crossed for Hector Hernandez to score.
In the dying moments, Atletico, who are joint leaders of La Liga with Barcelona, got the winner through a Alderweireld header from a Gabi Fernandez free kick.
There was no dream ending for Olimpic de Xativa after an efficient performance from a second-string Real Madrid secured a 2-0 win at the Bernabeu which sent them through to the last 16.
Real Sociedad also reached the next round with a 4-0 win over lower league Algeciras to seal a 5-1 aggregate victory.
Third division Racing Santander pulled off a shock as they beat Sevilla 2-0 away to go through 2-1 on aggregate.