Ikechukwu Uche had an early chance for the home side, but guided his header over. However, he managed to find the net for the opening goal with a right-footed shot from the edge of the area.
Giovani dos Santos continued the home dominance with a third just after the break as he stroked in from close range.
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However, Valencia found a way back into the match when Ricardo Costa nodded in.
However, Villarreal made sure of the points with six minutes remaining as Dos Santos grabbed his second of the match.