The La Liga outfit, recently promoted from Spain’s Segunda Division, provided a stern test for Oscar Garcia’s side but it would have proved a beneficial work-out ahead of the season opener against Leeds United next Saturday.
Indeed, there were spells where Albion matched their opponents, but the Yellow Submarine always looked dangerous and took control of the game with a two-goal burst inside six second-half minutes.
The game started on a sombre note in memory of the victims of the Spanish rail crash on Wednesday, which was impeccably observed by Seagulls fans.
But the volume was raised when Ashley Barnes raced onto a Leonardo Ulloa knock-down to clinically volley home with just two minutes on the clock.
Villarreal responded three minutes later but playmaker Cani’s low effort was beaten away by Tomasz Kuszczak, and to complete breath-taking start, Andrea Orlandi latched onto a superb through ball from Will Buckley, only to see his effort cleared to safety.
Inevitably, the Spaniards looked comfortable in possession and dangerous on the break, and it took a Matthew Upson deflection to prevent Jonathan Pereira getting a clean strike at goal.
Perez also had a dipping 20-yard effort tipped over by Kuszczak, and from the resulting corner Pereira rattled the crossbar.
As the half wore on, Albion saw more of the ball and Buckley went close with a shot on the turn following good work down the right from Crofts.
Kuszczak was again called into action to keep out a 25-yard free-kick from Bruno Soriano but there was nothing he could do to keep out Cani’s 40th minute drive, which took a deflection as it flew in.
Ulloa almost handed Albion the lead two minutes before the break when he lifted the ball over the advancing keeper Sergio Asenjo – but Mario Gasper was covering to hook the ball clear from under the bar.
Villarreal made four changes at the break, with Casper Ankergren also replacing Kuszczak for the Albion, and the half took some time to get going.
Indeed, Adam Chicksen – making his home debut – Adam El-Abd and Jake Forster-Caskey had also entered the fray before we saw the first strike on goal – Manuel Trigueros drilling the ball wide on 64 minutes.
Villarreal then showed their class to take the lead two minutes later when Pereira met a delightful back-flick from Perbet to drill home from close range.
With their tails up, the visitors found an extra gear and Pedro Rios made it three on 72 minutes when he tucked home following a surging right down the right from fellow sub Javier Aquino.
Inigo Calderon looped an effort onto the bar late on, but there would be no late comeback for Albion, who now look forward to facing Norwich at the Amex on Tuesday night – the final pre-season fixture before the big kick-off.
Albion: Kuszczak (Ankergren 45); Saltor (Chicksen 60), Upson (El-Abd 61), Greer (Dunk 79), Calderon; Crofts (Forster-Caskey 61), Bridcutt (Ince 90), Orlandi (March 70); Barnes (Barker 79), Ulloa, Buckley Dickenson 79).
Villarreal: Asenjo (Juanto 73); Gaspar (Alic 79), Musacchio, Pantic, Costa (Pina 46); Soriano (Rios 46), Trigueros (Ramos 79), Perez (Aquino 46), Cani (Jokic 46), Perbet (Juanto 73), Pereira Rodriquez (Camara).