French striker Jeremy Perbet fired the newly promoted side to a 22nd minute lead on Saturday before Javier Aquino doubled the advantage only eight minutes later.
Substitute Ikechukwu Uche scored the third goal for the Yellow Submarine with 15 minutes left.
The win provisionally lifts Villarreal to top of the league on nine points with four teams on six points set to play on Sunday.
A solitary strike from defender Marc Valiente was enough to secure Valladolid a 1-0 win against Getafe.
Valiente's 47th-minute winner meant the hosts picked up their first win of the season after starting with two losses.
Meanwhile, Celta Vigo drew 1-1 with Granada despite dominating possession and chances on goal.
Rafinha got Celta off to a perfect start with a goal on 29 minutes but Granada equalised through Piti in the second half.
It was a disappointing result for Celta, who dominated possession and fired in 17 shots to Granada's three efforts on goal.