Leading 1-0 from the first leg in Madrid on Wednesday, Valladolid were pegged back just before half-time when Fernando Sales headed the visitors level on aggregate.
However, Javi Guerra, who had scored the winner at Santo Domingo earlier in the week, was on target again six minutes after the break to ensure a return to the top flight after a two-year absence.
Miroslav Dukic's men had missed out on automatic promotion by just three points as they finished third behind Celta Vigo and champions Deportivo La Coruna, a full nine points ahead of Alcorcon in fourth.
