The 'Yellow Submarine' took home all three points thanks to a late winner from midfielder Fornals.
The goal came from a Real corner from which the visitors countered at pace.
Denis Cheryshev raced away down the left and fed Enes Unal, but the former Manchester City man was denied by Keylor Navas.
You could have been forgiven for thinking that the chance was gone at that point, but Fornals latched onto the loose ball on the edge of the box and deftly dinked the ball over the stranded Costa Rican and into the back of the net to give his side a shock victory.
It was a fine finish from the former Malaga man.
Check out the strike for yourself below:
Que jodido golazo acaba de hacer Fornals. 0-1 en el 88, y el @VillarrealCF que vuelve a hacerlo. Que vuelve a dar la campanada.pic.twitter.com/oFvIzga61f
— Daneil Doménech (@DaneilDomenech) 13 January 2018