Villarreal started brightly and had an early opportunity to take the lead when captain Gerard Moreno lifted the ball over the crossbar from close range.
Alaves gradually found their rhythm and registered the first shot on target through Lucas Boye, whose powerful effort forced Luiz Junior into a save.
Villarreal threatened again before the half-hour mark when Tajon Buchanan unleashed a long-range effort, but Alaves goalkeeper Antonio Sivera reacted brilliantly to tip the ball over.
That save proved important as Alaves struck moments later.
A well-worked passing move opened up the Villarreal defence, with Angel Perez delivering a clever pass from the byline for Boye. The striker made no mistake from eight yards, calmly finishing to put the hosts ahead.
Villarreal had a chance to respond before the break, but Moreno could only fire his effort straight at Sivera from just outside the six-yard box.
The second half was a scrappy affair, although Villarreal continued to search for an opening. Nicolas Pepe created space after a strong run into the final third, but his shot lacked power and was comfortably saved by Sivera.
Alaves then came close to doubling their lead on the counter-attack. Perez found himself in space and fired from a tight angle, only to see his effort crash against the post.
Villarreal stepped up the pressure as the final stages approached, forcing Alaves deeper. Sivera stood firm, making an important block to deny Pepe before producing an outstanding save to keep out a powerful effort from Ayoze Perez.
The visitors went even closer in the closing moments when Juan Foyth struck the post with an instinctive effort, but Alaves survived the late onslaught.
The result means Alaves have avoided defeat in their first three LaLiga matches for the first time in seven years.
Villarreal, meanwhile, are still waiting for their first victory of the campaign. Inigo Perez remains without a win after three games in charge, while the Yellow Submarine have now failed to win any of their last six away matches stretching back to last season.
