The Brazilian Leo Baptistao netted the only goal of the game early in the second half. Villarreal are three points behind group leaders Rapid Vienna, who won 1-0 away to Dinamo Minsk.
Villarreal plays at winless Levante on Sunday, while Barcelona — still without Lionel Messi — is at Sevilla and Real Madrid faces a difficult game at city rival Atletico Madrid.
Unbeaten and playing some entertaining football, Villarreal has 16 points from six games, one more than Barcelona and two more than Real Madrid.
The team from eastern Spain, whose best-ever result in the Spanish league was a second-place finish in 2008, has been relying on solid defense to keep its momentum going.
"It's been key in all matches we have played," Villarreal coach Marcelino Garcia Toral said. "We defended very well against Athletic Bilbao and Atletico Madrid, which are very powerful clubs, so it means that we can definitely defend well."