However, they may by now be rueing letting the London club off the hook.
It looked like being a joyous night for Villarreal manager Unai Emery against the club which sacked him in 2019 as his side reached half-time with a 2-0 lead.
It was all thanks to goals by Manu Trigueros and Raul Albiol.
And when Arsenal had Dani Ceballos sent off just before the hour mark it looked bleak for the visitors.
Arsenal were rocking and needed goalkeeper Bernd Leno to avoid them slipping further behind but they were thrown a lifeline when Nicolas Pepe converted a 73rd minute penalty kick.
A chaotic game took another twist as Villarreal were also reduced to 10 men when former Tottenham Hotspur player Etienne Capoue received a second yellow card.
Villarreal, coached by a Europe League specialist in Unai Emery, maintained their 100 percent home record in the competition this season.
But it was a bittersweet night for the La Liga side with the tie delicately balanced ahead of next week’s return.
Emery won three successive Europa League titles with Sevilla between 2014 and 2016 and his Villarreal side have remained unbeaten in the competition this season.
They enjoyed a dream start as defender Juan Foyth surged forward in the fifth minute and played in Samuel Chukwueze on the right.
His ball in fell for Trigueros who lashed an unstoppable low drive into the bottom corner.
Veteran Albiol made it 2-0 on the half hour mark when a corner-kick was flicked on and he arrived unmarked at the far post to volley high past Leno from close range.
Arsenal thought they had a route back into the game shortly afterwards when Foyth tripped Pepe in the area.
A penalty kick was initially awarded but a VAR check showed that Pepe had handled the ball earlier in the build-up.
Mikel Arteta’s side pressed early in the second half but their momentum was halted when Ceballos caught Daniel Parejo on the foot and was shown a second yellow card.
Emery’s side went for the jugular and Arsenal were indebted to Leno for a great save which prevented Gerard Moreno making it 3-0.
The complexion of the tie changed, however, when Bukayo Saka drew a foul in the penalty box and Pepe drilled his kick straight down the middle to halve the deficit.
Capoue’s evening came to an undignified end as he injured himself with a wild tackle on Saka and was shown a second yellow card while being taken off on a stretcher.
There was still time for substitute Pierre-Emerick Aubameyang to miss a chance to make it 2-2 but after what looked like a dreadful position, Arsenal’s season remains alive.
“We didn’t want to come here and lose but after the way the game developed, you have to take the result,” Arteta said. “If you have to lose it is probably the best result we could have.
“I am confident we have a chance to win.”
Manchester United crushed AS Roma 6-2 in the first leg game of the other semi-final pairing
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