Arnaut Danjuma's eighth-minute goal gave the Spanish Europa League champions the win and Unai Emery's men were unlucky not to take an even greater league to Munich next week.
Danjuma opened the scoring in the eighth minute when he was in the right place to get a touch on Dani Parejo's effort to direct the ball past Manuel Neuer.
Villarreal were looking confident and looking to take the game to Bayern, who had plenty of the ball, but didn't seem to have much idea what to do with it, reports Xinhua.
Coquelin thought he had doubled Villarreal's lead four minutes before the break when his cross from the left beat Neuer and floated into the far corner of the net, but the goal was ruled out because striker Gerard Moreno was offside in the buildup.
Things didn't improve for Bayern in the second half with Moreno intercepting a poor pass from Neuer and sliding the ball just wide from 40 meters while at the other end, Pau Torres got a head on the ball to deflect Coman's goalbound effort.
Moreno then hit the post from 20-meters as the game remained wide open, with Bayern looking to attack, while Villarreal tried to take advantage of the spaces they left on the break.
There were no further goals and the tie will be decided next Tuesday (IST) in Germany.
--IANS
inj/
(This story is published as part of the auto-generated syndicate wire feed. No editing has been done in the body by ABP Live.)