The home side almost took the lead in surprising fashion after 20 minutes when Barcelona loanee Gerard Deulofeu took a corner and hit the post.
Chances were few and far between in the rest of the first half as Sevilla's unbeaten home run of 12 league games came up against a Villarreal outfit who haven't suffered defeat on the road for six games.
Uche had another opportunity 10 minutes into the second half, this time shooting just wide from inside the box.
Sevilla were struggling to break the Yellow Submarine down and the visitors struck what looked to be the winner with 10 minutes left on the clock.
Some slick one-touch passing resulted in Luciano Vietto going through on goal and he coolly dinked the ball into the far corner.
It looked as if Sevilla's unbeaten home run would come to an end until another Barcelona loanee, Denis Suarez, found the bottom corner after a scramble in the box.
Villarreal lose their six-game unbeaten record away from home and miss out on the chance to move into the top six.