كتب : Mohamed Sabe
Former Real Madrid midfielder Carlos Diogo scored what proved to be the winner for Zaragoza in the 78th minute.
The Uruguayan international guided the ball home past reserve keeper Albert Jorquera.
Zaragoza had eliminated Barcelona from the same stage with a 5-4 aggregate win last season
Earlier in the day, Deportivo La Coruna crushed Valladolid 4-1 to edge closer to the semi-finals.
Second-division Valladolid took the lead through Vladimir Manchev in the first-half.
Depor responded with strikes from Pablo Alvarez, Ruben Rivera, Joan Verdu and Juanma after the break.
Getafe also beat Osasuna 3-0, courtesy of strikes from Daniel Guiza, Alexis and Maris Verpakovskis.
Sevilla will face Real Betis in the fourth quarter-final first leg on Thursday.