Villarreal may have had more possession and more shots, but it was defending champions Sevilla who scored the most goals to win the match 2-1 on the night and go through 5-2 on aggregate.
Ibarra and Suarez scored for Sevilla, Dos Santos for Villarreal, with all the goals coming in the second half.
Villarreal finished the match with ten men after Bailly was red-carded in the 77th minute.