Levante goalkeeper Keylor Navas was shown a straight red card in the 10th minute at the Ciutat de Valencia stadium when he felled forward Uche in the penalty area.
Midfielder Bruno, whose polished performances this season have prompted calls for him to be included in the Spain squad, stroked the ball into the net past hastily-introduced replacement keeper Javi Jimenez.
With an extra man, Villarreal created and squandered a host of chances before Bruno threaded a pass through to Uche in the 74th minute and he fired a clinical shot low into the corner.
The pacy Nigerian then scored the goal of the game a minute from time when he netted a spectacular overhead kick.
Fourth-placed Villarreal, who spent a season in the second division last term and finished second behind Elche, have 27 points from 14 matches, seven behind Real Madrid in third after they thrashed promoted Almeria 5-0 on Saturday.
Unbeaten leaders Barcelona and second-placed Atletico Madrid also recorded thumping wins, Barca beating Granada 4-0 at the Nou Camp and Atletico hammering Getafe 7-0 at the Calderon.
(Reporting by Iain Rogers, editing by Ed Osmond)
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