Danjuma scored the opener from the penalty spot in the 10th minute.
The Dutch forward who was overlooked for the Nigerian senior national team by former head coach Gernot Rohr had a shot saved with a minute before half time.
Super Eagles star Samuel Chukwueze was introduced at the start of the second half in place of Yeremi Pino.
Senegal striker Boulaye Dia replaced Arnaut Danjuma with 19 minutes left to play in the game.
In the 80th minute, nimble-footed Chukwueze was presented with a chance to grab the third goal of the night when he latched onto a long pass from his own half but his eventual low shot missed target by whiskers.
The winger has now made 22 appearances overall in the La Liga accumulating 984 minutes of playing time.
The Diamond Academy FC of Umuahia product has started in eight league appearances and been mostly used in a substitute role this season.
Ahead of their next match, a trip to Anfield to face Liverpool in the semifinals of the UEFA Champions League, Villarreal are now five games unbeaten in all competitions.
Izuchukwu Michael
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