It was a difficult final minutes for Arsenal who needed to score a goal to move on.
For the first time, Villarreal has reached a final in a European Cup and it was wild Spanish joy at the Emirates led by Unai Emery who coached Arsenal from May 2018 to November 2019 when he was fired.
The Arsenal players walked with lowered heads, empty eyes and sat down on the grass after the five minutes of extra time had been completed.
Villarreal will now face Manchester United in the Europa League final in Gdansk, Poland, on May 26.