Two of Dortmund's four winning goals were scored by Serhou Guirassy, while Karim Adeyemi and Daniel Svensson each contributed one goal, according to UEFA records.
This victory took Dortmund up to fourth place in the Champions League standings with 10 points from five matches.
On the other hand, this crushing defeat has seen Villarreal drop to 34th in the Champions League standings after only collecting one point from five matches.
Villarreal actually managed to break through Dortmund's goal first through Tajon Buchanan, but the referee disallowed the goal due to offside.
Dortmund were able to take the lead in first-half stoppage time through a goal scored by Serhou Guirasssy, making the score 1-0 in the 45+2 minute.
