Samuel Chukwueze was on from start to finish as Villarreal extended their unbeaten run at home to seven matches.
The Yellow Submarine currently sit sixth on the log and hope to finish high enough to get a UEFA Champions League spot. Villarreal are currently three points off the top.
Daniel Parejo scored in the 64th minute to give Villarreal their win in a game that saw Chukwueze complete 70% of his 33 passes.
The Nigerian had 60 touches and made two key passes in the game but failed to complete any of his accurate long balls.
Chukwueze had two shots off target and completed nine of his twelve dribbles.
The winger won 60% of his 20 ground duels and lost possession twenty times in the game. He was also fouled two times in the encounter.
Chukwueze has been invited to the Super Eagles as part of the 30-man squad to face Ghana in the final phase of the World Cup qualifiers. Both games will come up on the 25th and 29th of this month with the first leg to be played in Accra while the second leg is scheduled to come up in Abuja.