The visitors started well and they took the lead through Antoine Griezmann's first-half penalty, only for substitute Enes Unal to pull Villarreal back into contention with eight minutes to play in Castellon.
The controversy was not to stop there either, as Unal prodded home deep into injury time in order to hand Villarreal a shock 2-1 comeback win.
Relive all of the action with our minute-by-minute updates below.
"There's no way of knowing that in a squad of 25, six could be injured, nothing is guaranteed in life. Obviously you are always prepared to solve situations that you may encounter. I'm not worried, I have a small but important squad. We will compete with the guys that are available."
VILLARREAL STARTING XI: Asenjo; Mario, Bonera, Alvaro, Costa; Trigueros, Rodrigo, Soriano; Fornals, Bacca, Raba
ATLETICO MADRID STARTING XI: Oblak; Vrsaljko, Gimenez, Godin, Lucas; Thomas, Saul, Correa, Koke; Costa, Griezmann