Goals either side of half-time from Roque Santa Cruz and Sergi Darder saw Malaga to the win at their Estadio La Rosaleda home.
Victory lifted Malaga – who finished the clash with 10 men – into 11th in the La Liga table, while Villarreal sit seventh and two points adrift of Real Sociedad.
A win would have taken Marcelino's Villarreal team into sixth – the final European place in La Liga.
The hosts needed just six minutes to take the lead as Samu cleverly slipped in Santa Cruz, who finished from a tight angle.
Malaga doubled their lead in the 53rd minute thanks to a lightning counter-attack.
Nordin Amrabat was released down the left and, after beating his defender, waited for the late run of Darder, who finished well from inside the area.
Amrabat made life difficult for his side with 16 minutes remaining when he saw red.
The Morocco international, on loan from Galatasaray, felt he was fouled on the wing before indicating to Alfonso Alvarez that the referee needed glasses, with the official showing him a straight red card.
