The away side were given an opportunity to take the lead after 10 minutes when Keilor Navas gave away a penalty and saw red for a tackle inside the area.
Bruno Soriano stepped up and buried the spot kick into the bottom left corner to make it 1-0 after 13 minutes.
Villarreal dominated after the sending-off and came close to making it 2-0 on 26 minutes, though Cani could only direct his volley wide of the post.
Hernan Perez almost doubled Villarreal's advantage on 40 minutes, but his first-time shot smashed the crossbar.
Soriano came close again just before half time, but his shot from the edge of the box was saved well.
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Ikechukwu Uche found space in the box on 75 minutes and fired the ball into the bottom corner to make it 2-0.
David Barral came close with a header on 77 minutes for Levante, but he could only direct it over the bar.
Uche added a third on 89 minutes, firing past the goalkeeper to secure all three points.