The Yellow Submarines were no match for their relegation-threatened visitors.
Nigerian winger Samuel Chukwueze and Villarreal continue their crash under new manager Quique Setien.
The Yellow Submarines are still waiting for a first win under Setien after a disappointing 2-0 defeat at home to Real Mallorca.
Nigerian international Chukwueze was in action from start to finish but was caged by the well-drilled Mallorca defense.
The 24-year-old attempted four shots, hit the woodwork once but failed to create a singe chance in 90 minutes.
Chukwueze remains without a goal this season in 12 appearances, with just an assist to his name.
Villarreal continue winless run under Setien
The Yellow Submarines wait for a first win under Setien has been extended by another week after a poor outing on Sunday night.
Villarreal proved to be no match for Mallorca, who came, saw and conquered their host with a solid performance.
Two goals in either half from man of the match, Vedat Muriqi, who also got an assist, and Amath Ndiaye handed the relegation side a comfortable win on the night.
Villarreal dominated the encounter from start to finish but a clinical display from the visitors means Setien will have to wait a while longer for his first win since he replaced Unai Emery.