Photo courtesy of Alaves Facebook page.
The hosts snatched victory through Manu Sanchez's early goal, but had to battle in the second half after goalkeeper Antonio Sivera was dismissed before the hour mark for handball outside of his area.
The stopper was also hurt as he challenged Ayoze Perez in the incident, crashing his head into the forward's knee, and taken to hospital for analysis after being sent off.
Villarreal, fifth and trailing Athletic Bilbao in fourth by four points, took 24 shots but only managed to get two of those on target.
Alaves survived 15 minutes of stoppage time in torrential rain to secure a vital win in their bid to avoid relegation, despite suffering a second red card.
Antonio Blanco was dismissed in the 94th minute for apparent dissent, but his team claimed the three points and climbed provisionally 17th, two points above the drop zone.
Alaves had gone 14 league games without a clean sheet and this was their first win in seven.
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