Following a tense second-leg battle, Villarreal progress to the Europa League final based on aggregate, following a goalless draw at Emirates Stadium.
Aubameyang had the best chance of the first half to put the Gunners in front and another chance in the second half but he struck the left post twice.
Arsenal showed more intent in the second half as Smith Rowe and Holding both close to scoring.
Arsenal threw everything at Villarreal in the closing stages, butstood its ground to book a place in the final.