The Brazilian raced through onto Borja Valero's pass in the 51st minute and, under pressure, lobbed visiting goalkeeper Dudu Aouate to score his tenth goal of the season.
Juan Carlos Garrido's side have 33 points from 16 games, seven behind leaders Barcelona. Real Madrid are second with 38 points and host Sevilla on Sunday.
Villarreal's neat possession football is reminiscent of Pep Guardiola's Barca side and one such passage of play ended with Santi Cazorla volleying home in the 11th minute.
Jonathan de Guzman equalised against the run of play with a spectacular shot in the 28th minute, but it was a rare sight of goal for the visitors and Italy's Giuseppe Rossi restored Villarreal's advantage from the penalty spot in the 35th.
In other games, Athletic Bilbao climbed to sixth on 25 points after a 2-1 away at Levante, and Deportivo Coruna drew 1-1 at home with Sporting Gijon.
