Roger Schmidt's side controlled much of the game but never looked like scoring against their Spanish guests. Bayer Leverkusen have now won just one of their last six games.
Bayer Leverkusen 0-0 Villarreal (0-2 aggregate)
Bayer Leverkusen were knocked out of the Europa League after failing to overturn a 2-0 first leg score against Villarreal, in a 0-0 draw at the BayArena on Thursday night.
Two goals from Cedric Bakambu at the Estadio El Madrigal a week before proved enough following a second leg that saw Roger Schmidt's side huff and puff throughout the match, but ultimately fail to break through Villarreal's defense.
Schmidt's side controlled possession and showed far more initiative throughout the match but never looked as though they were up to the task of overturning the two-goal deficit.
Leverkusen's only real chance in the first half came when a cross bounced to the feet of Marlon Frey in front of the Villareal goal, moments before the break. In an incident that was emblematic of Leverkusen's play in general, the youngster swung at the ball but fired it over Sergio Asenjo's crossbar.
Unfortunately for Schmidt's side the second half didn't offer any solace, as the Bundesliga side continued to push down each wing before firing aimless crosses in to the box with the hope that star striker Javier Hernandez would produce a goal out of thin air.
Ultimately it was the visiting side that looked more inclined to score, as Bakambu enjoyed sporadic counter attacks with Roberto Soldado and later Manuel Trigueros - who had a last-minute shot cleared off the Leverkusen line from Andre Ramalho.
In the end it was a game that Leverkusen never looked like winning in a tie that had long since finished in Villarreal's favor.
Now, having won just one of their last six games in all competitions, Schmidt and his squad will shift their focus to the Bundesliga and Sunday's away match in Stuttgart, when they continue their struggle to qualify for a European berth for next season.