That leaves Francis Coquelin, formerly of Arsenal, to drop to the bench, with Dani Parejo starting in midfield.
Emery was expected to have star winger Samuel Chukwueze fit and available again but he is not even among the substitutes.
Elsewhere, Gerard Moreno will be is partnered up front by Carlos Bacca, with Paco Alcacer left on the bench.
Geronimo Rulli is the cup goalkeeper, meaning Sergio Asenjo will sit on the bench.
Villarreal starting XI (4-4-2): Rulli, Foyth, Albiol, Pau Torres, Pedraza, Parejo, Capoue, Trigueros, Moreno, Bacca, Pino
Injury list: Iborra
Doubts: Chukwueze, Foyth
Villarreal Europa League squad
Goalkeepers: Sergio Asenjo, Geronimo Rulli, Iker, Filip Jorgense, Marc Vidal
Defenders: Mario Gaspar, Raul Albiol, Pau Torres, Ramiro Funes Mori, Juan Foyth, Pervis Estupinan, Alberto Moreno, Ruben Pena, Jaume Costa, Dani Esmoris, Edu Adell, Vadim Murria Soriano, Andrei Ratiu
Midfielders: Daniel Parejo, Samu Chukwueze, Daniel Raba, Manu Trigueros, Francis Coquelin, Moi Gomez, Alfonso Pedraza, Etienne Capoue, Diego Collado, Carlo Garcia, Alex Baena, June-Hyuk Ahn, Juan Agüero, Alejandro Millan, Haissem Hassan
Forwards: Gerard Moreno, Carlos Bacca, Paco Alcacer, Yeremi Pino, Fernando Nino