Villarreal, with former Arsenal coach Unai Emery on the bench, got off to a real dream start to the match.
Already in the fifth minute of the match, midfielder Manuel Trigueros put 1-0 behind Bernd Leno in the Arsenal goal.
After just over half an hour, it also came 2-0 when Raul Albiol pushed the ball in from close range after a corner.
Ceballos expelled
In the second half, Arsenal's Daniel Ceballos received his second yellow card after a late tackle on Villarreal's Daniel Parejo.
A decimated Arsenal were then awarded a penalty kick after Bukayo Saka was sent off in the penalty area.
Nicolas Pepe stepped forward and coolly scored an important 2-1 goal.
In the 80th minute, Villarreal would also get a man sent off.
Etienne Capoue came in late in the match, which resulted in a second yellow card.
The final result was also 2-1 and it is now completely open for the return meeting on 6 May.
ARCHIVE: Benzema saved cross after dream goal (April 28)
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Karim Benzema scored the equalizer.
Photo: Bildbyrån / Rörligt Viaplay