The match ended with a 1:1 draw: Villareal's Gerard Moreno scored in the 29th minute, while Manchester United's Edinson Cavani in the 55th minute.
The epic penalty shootout ended with the 11:10 victory of Villareal.
With this victory, Unai Emery set a new landmark as the most-titled coach in UEFA Cup/UEFA Europa League history.
The match was held at the Arena Gdansk in Poland on late Wednesday.