Bilbao won 1-0 at home to Alcoyano to seal a 2-1 aggregate victory in their last-32 tie, with striker Borja Viguera striking the only goal of the second leg at the San Mames.
Viguera's 39th-minute goal ended the run of third-tier Alcoyano, with the Basque club set to face Celta Vigo for a spot in the quarter-finals.
Elche snuck past Real Valladolid 1-0, as Adrian's seventh-minute goal in the second leg at the Estadio Manuel Martinez Valero the difference.
It marked the 26-year-old midfielder's first goal of 2014, and his first for Elche - after switching from Rayo Vallecano in the off-season.
Elche won 1-0 on aggregate, after their trip to Vallecano in the first leg ended goalless - earning them a date with Barcelona in the round of 16.
Atletico eased into the last-16 - where they meet bitter rivals Real - with a 5-2 aggregate victory over L'Hospitalet.
After winning the first leg 3-0 away at the Segunda B outfit, Diego Simeone's men led twice at their Vicente Calderon home - only to be pegged back for a 2-2 draw.
Mario Mandzukic struck twice for Atletico, but Ruben Alcaraz's brace for the visitors earned them a draw on the night.
Malaga thrashed Deportivo La Coruna 4-1 to earn a 5-2 aggregate victory, and move into a clash with La Liga counterparts Levante.
With the tie at 1-1 after 90 minutes, but slight in Malaga's favour due to the away goals rule, the outcome was evenly poised after a scoreless 45 minutes at La Rosaleda.
The tie was bound for extra time even, as Roque Santa Cruz's opener for Malaga was cancelled out by Helder Postiga's 57th-minute equaliser.
But a Malaga barrage saw them finish over the top of Deportivo, as Recio put them ahead again two minutes later before Santa Cruz's second in the 68th minute all but sealed the tie.
Ignacio Camacho's late goal was the icing on top of the victory.
