It was a spirited performance in the return match from Gijon, who had lost the first leg 2-0, especially in the second half with substitute Alen Halilovic grabbing a double, including a penalty.
Bernardo Espinosa nodded Gijon in front with a free header from a corner after 14 minutes but Van Wolfswinkel finished clinically four minutes later at the other end after a good team move.
Barca youth product Halilovic came on at halftime and slotted home almost immediately.
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He was then on target again, sending keeper Daniel Gimenez the wrong way with a penalty following a handling offence by Alfred N'Diaye after 72 minutes.
Gijon, though, left gaps at the back and the visitors took advantage with a Van Wolfswinkel header and an effort from Alvaro Cejudo.
Juan Dominguez headed Deportivo La Coruna in front against second-tier Llagostera but he was also guilty of conceding a penalty, scored by Jordi Lopez, in a 1-1 draw that took the top- flight side through 3-2 on aggregate.
Burgui and Felipe Caicedo netted as Espanyol came from behind after a Verza opener to beat Levante 2-1 and win 3-2 overall.
Ciro Immobile and Jose Antonio Reyes gave Sevilla a comfortable 2-0 win over Logrones, 5-0 on aggregate.
Holders Barcelona are already through after beating Villanovense, the tie having been brought forward due to their participation in the Club World Cup.
Real Madrid have been thrown out after fielding the ineligible Denis Cheryshev in their first leg against Cadiz.
(Editing by Tony Jimenez)
