The score line opened with a lethal strike from Bundesliga top scorer for the ongoing season, Robert Lewandowski.
Villarreal however replied with a counterattack equaliser carefully placed above Neuer by Nigerian international, Samuel Chukweze, making it 2-1 on aggregate.
The la liga side who are currently 7th on the league table, will now proceed to the next rounds of the competition, as the first semi-finalists.