The goal of the Castellon team was the work of Santi Cazorla, also a penalty.
The Mallorcanist triumph, which joins those achieved also at home against Eibar, Espanyol and Real Madrid, away from the dangerous area of the table.
He Villarreal, for his part, chains his third game without winning and leaves him, another day, unable to add his 300th victory in the highest category of Spanish football.
Kubo was a nightmare for him "Yellow Submarine" on a day marked by the three penalties indicated, rain and cold.
The Japanese, given by Real Madrid, began failing three passes in the first minutes, but it was decisive to cause the play of the penalty that transformed Lake Junior and score the third goal of his team.
The maximum penalty, second in which Kubo is the protagonist after the one he generated against Athletic Bilbao -flaked by Abdon Prats-, fIt was very protested by Villarreal, like the second penalty, decreed by the referee after a fall of Aleix Febas in the area, shot down by goal Sergio Asenjo.
The VAR intervened to analyze the action of Kubo and after a minute and a half of waiting he gave his approval to the decision of the referee Del Cerro Grande.
In the fall of Febas, the referee interpreted that Asenjo swept the Mallorcanist when he finished the goal, and his decision was also endorsed by the video arbitration.
Villarreal, who had started better than his rival, lost 2-0 before the first half hour of the game, and got down to work immediately to cut distances on the scoreboard.
Cameroon Andre Zambo Anguissa had the best chance (min. 39), but he did not know how to solve the goal Manolo Reina, and in 45, Ghanaian Lumor Agbenyenu saved his team clearing a shot of Mario Gaspar in the same line of goal.
Both visitor plays were stamped by internationals Santi Cazorla and Gerard Moreno, both protagonists of the most dangerous actions for Mallorquinists.
The second part began with the third penalty, this time, favorable to the people of Castellon, which Cazorla materialized deceiving Reina.
Everything seemed expensive for visitors and when they played best, with the Nigerian Samuel Chukwueze on the site of Vicente Iborra, came up again, the magic of Kubo to score from outside the area his first goal with Mallorca and place 3-1 on the scoreboard.
The Japanese, who until now would have only shown details of the class he treasures, was decisive in his best game with the vermilion shirt until was replaced (min. 65) by Josep Sene in the middle of a thunderous ovation.
Mallorca backed down in the final phase of the game with the objective of preserving the comfortable income that it had and, with it, it was at the mercy of a Villarreal who looked hard for the Queen's goal.
Despite the effort made by Javier Calleja's team in search of a goal that put them in the game, the vermilions were very solid in defense until mooring a very important triumph in their objectives to escape the positions of the descent.
3-Mallorca: Queen; Joan Sastre, Valjent, Raillo, Lumor (Xisco Campos, min. 84); Kubo (Sene, min. 65), Baba, Dani Rodriguez, Febas; Junior Lake, Budimir (Abdon Prats, min. 82).
1-Villarreal: Asenjo; Mario Gaspar (Trigueros, min. 80), Albiol, Pau Torres, Pena; Cazorla, Anguita, Iborra (Samuel Chukwueze, min. 46), Moi Gomez (Ontiveros, min. 67); Gerard, Toko Ekambi.
Goals: 1-0, min. 12: Junior Lake of penalty; 2-0, min. 23: Dani Rodriguez, of penalty; min. 47: Santi Cazorla, of penalty; 3-1, min. 52: Kubo.
Referee: From Cerro Grande (Madrid Committee). He admonished Dani Rodriguez, Febas, of Mallorca; to Asenjo and Pena del Villarreal.
Incidents: Match corresponding to the thirteenth day of LaLiga played at the Son Moix stadium before 8,348 spectators. Del Cerro Grande demanded that the security agents surrounding the pitch change the yellow vests they wore (because of the rain), so as not to be confused with the colors of Villarreal.