Diego Castro put the visitors ahead after just six minutes at Camp El Madrigal.
Moroccan international Abdelaziz Barrada made a strong run down the right wing before crossing well to Nicolas Fedor in the penalty area. Fedor's deft first touch created space for a shot, but he unselfishly played in Castro, whose simple finish beat Diego Lopez in the Villarreal goal.
Villarreal got back on level terms just before the interval when Nilmar converted from the penalty spot, but Barrada's goal in the 72nd minute sealed all three points for Getafe.
