The Yellow Submarine have not been short of goals this term, and they made a bright start to proceedings, but squandered an early chance to hit the front when captain Gerard Moreno lifted the ball over the bar from close range.
The first shot on target of the night fell to the hosts, as a firm strike from Lucas Boye forced Luiz Junior to parry the ball away from danger.
Shortly before the half-hour mark, Canada international Tajon Buchanan came close to edging Villarreal in front in spectacular fashion when his long-range shot was superbly tipped over the bar by Antonio Sivera.
That proved a crucial intervention, as moments later Alaves broke the deadlock with the next attack of the match. Following an impressive pass and move sequence, Angel Perez’s smart pass from the byline found Boye, who duly slotted the ball home in confident fashion from eight yards out.
Villarreal could, and perhaps should, have equalised with the interval on the horizon, but Moreno’s strike from just outside the six-yard area was straight at Sivera.
The opening stages of the second half were scrappy, with the main flashpoint being the enforced substitution of Alaves’ Toni Martinez due to injury. Nicolas Pepe managed a shot on target after a great run into the final third, but his effort lacked conviction and resulted in a comfortable save for Sivera to keep the hosts in front.
With just over 20 minutes remaining, Quique Sanchez Flores’ side came within a whisker of doubling their advantage on the counter, but after the ball fell nicely into the path of Perez, his rapid strike from an acute angle cannoned off the post to the relief of Villarreal’s travelling support.
As full time loomed, Villarreal’s urgency notably increased and the hosts’ defence came under intense pressure. Sivera made a vital block to deny Pepe before the goalkeeper produced a world-class save to prevent Ayoze Perez from equalising late on with a rocket of a strike.
With time running out, the woodwork then came to Alaves’ rescue as Juan Foyth’s instinctive shot on the turn struck the post to the anguish of the visitors.
Despite that late surge of big chances for Villarreal, Alaves held on for a victory, meaning they’ve avoided defeat in their opening three games of a LaLiga campaign for the first time in seven years.
Meanwhile, Inigo Perez remains winless after three games as Villarreal’s head coach, while they have now failed to win any of their last six away matches across this season and last.
Flashscore Man of the Match: Antonio Sivera (Deportivo Alaves)