Nicolas Pepe's penalty provided a Europa League lifeline for 10-man Arsenal as they were beaten 2-1 by Unai Emery's Villarreal in a dramatic semi-final first leg in Spain.
Arsenal endured a dismal first half at Estadio de la Ceramica as poor defending allowed Manuel Trigueros to smash home from inside the box (5), before an unmarked Raul Albiol doubled Villarreal's lead from close range following a corner (29).
Arsenal were second best to their former manager's side and their hopes of reaching the final appeared in even greater doubt when Dani Ceballos was shown a second yellow card for planting his studs on Villarreal's Dani Parejo early in the second half.
But the Gunners were handed a scarcely-deserved route back into the tie when Bukayo Saka was tripped by Trigueros to win a penalty, with Pepe, who had been denied a spot kick earlier in the game due to a handball picked up by VAR, holding his nerve (73).
- How the teams lined up | Match stats
- Europa League fixtures | Results
- Europa League draw and schedule
- Get Sky Sports | Get a Sky Sports Pass
Villarreal then went down to 10 men themselves for the final 10 minutes as former Watford midfielder Etienne Capoue went in late on Saka to earn his second yellow card.
Mikel Arteta had opted to start the game without a recognised striker due to injuries, but Arsenal almost salvaged an unlikely draw when substitute Pierre-Emerick Aubameyang, who was only fit enough for the bench following his bout of malaria, was denied by Villarreal goalkeeper Geronimo Rulli in stoppage time.
A 2-1 loss, however, is a far better result than Arsenal's overall performance deserved and the opportunity is now there for them to go on a claim a place in the final in next week's second leg.
Villarreal: Rulli (7), Foyth (7), Albiol (7), Pau (7), Pedraza (6), Parejo (7), Capoue (5), Trigueros (7), Chukwueze (7), Alcacer (6), G Moreno (6).
Subs: Coquelin (7), Gaspar (6), A Moreno (6), Gomez (6).
Arsenal: Leno (7), Chambers (6), Holding (6), Mari (5), Xhaka (5), Partey (5), Ceballos (3), Saka (7), Odegaard (5), Smith Rowe (6), Pepe (7).
Subs: Martinelli (6), Aubameyang (6), Willian (n/a), Elneny (n/a).
Man of the match: Juan Foyth
How Arsenal clawed their way back
Arteta had expressed optimism about Arsenal's injured players returning in his pre-match press conference but Martin Odegaard was the only one who started, with Alexandre Lacazette and Kieran Tierney unable to even join Aubameyang on the bench.
Arsenal's lack of firepower would prove problematic but it was the absence of Tierney that hurt them for Villarreal's opener as makeshift left-back Granit Xhaka, together with Ceballos, backed off Samuel Chukwueze, allowing Trigueros to fire home from his deflected pass.
Emery, sacked by Arsenal in November 2019 after just 17 months in charge at the Emirates Stadium, pumped his fists in celebration in his technical area and the early setback rocked the visitors.
- Arsenal only made one change from Friday's 1-0 loss to Everton, with Martin Odegaard coming into the side and Eddie Nketiah dropping to the bench.
- Pierre-Emerick Aubameyang was fit enough for the bench but Kieran Tierney and Alexandre Lacazette were not available.
Arsenal's nervousness was apparent in stray passes and panicked touches as they attempted to play out from the back and there was a glaring lack of cutting edge at the other end, leaving Emile Smith Rowe with little to work with in the false nine position.
Arsenal didn't muster a shot until the 26th minute, when Saka curled wastefully over the bar, and their only other efforts of the first half involved Thomas Partey blasting a long-range effort into the stands and Rob Holding heading tamely wide from a free-kick.
Villarreal, meanwhile, continued to look threatening, springing forward every time they robbed Arsenal of possession and targeting the Gunners' left side, where Chukwueze and right-back Juan Foyth found themselves with plenty of space to work in.
It was from a set piece, though, that they struck their second as Arsenal left two men unmarked in their own six-yard box from a corner, Albiol tucking home Gerard Moreno's flick at the far post.
Arsenal were reeling but out of nowhere they were then awarded a penalty when Pepe was tripped and referee Artur Dias pointed to the spot, only for the decision to be overturned as a VAR review showed the Ivorian had handled the ball in the build-up.
Pepe would have to wait for his chance from the spot.
Ceballos picked up his first booking of the night shortly before half-time when he tripped Foyth following another Villarreal breakaway and Arteta was then punished for opting not to substitute him.
Ceballos, whose errors almost cost Arsenal in the round of 32 against Benfica, had been fortunate to avoid a second yellow card for a careless foul moments after the break but there was no reprieve for him when he left a foot in on Parejo soon afterwards.
It seemed Arsenal's hopes of reaching the Europa League final, their only hope of qualifying for next season's Champions League, were slipping away from them as Villarreal tried to press home their man advantage.
Bernd Leno made a smart save from Chukwueze to keep them in the tie and then made an even better one from Moreno after he had been played in on goal by former Arsenal man Francis Coquelin.
But Arsenal, buoyed by Leno's heroics, then won their potentially crucial penalty as Saka's trickery forced the error from Trigueros. Pepe slotted the spot kick down the middle.
Another layer of drama was added to a chaotic evening when Capoue saw red, injuring himself in the process, and a tie that had almost slipped away from Arsenal suddenly tilted in their favour.
The Gunners will need to show considerable improvement in next week's second leg at the Emirates Stadium if they are to advance to the final, where they would likely face Manchester United, 6-2 winners against Roma in the other semi-final, but Pepe's penalty has at least given them hope.
What the managers said...
Mikel Arteta: "We didn't want to come here and lose obviously but the way the game developed, being 2-0 down and with 10 men, it's probably the best result we could have.
"They were two different halves. In the first half, there were so many moments that we weren't us. We weren't clear with our high press, we were disorganised, we were not precise with the ball and we didn't have enough control.
"We didn't have enough threat or desire to attack the box but in the second half it was completely different.
"I am confident, we have a chance to win [the tie], that's for sure."
Unai Emery: "In the second half, we started with a little more defensiveness because they pushed it on us, but we had chances to score the third goal and that was our plan.
"The two expulsions changed the match, but the penalty is not a penalty.
"I think we deserved this victory. We deserved to do it with more difference [in the scoreline], but we play there again with the same plan, thinking of the control and to play with our personality and to take the performances into the second leg."
Opta stats: Arsenal's red mist
- Arsenal have been shown 10 red cards in all competitions under Mikel Arteta, twice as many as any other Premier League side in the period since he took over in December 2019.
- This was just the second time in their 10 European semi-finals that Arsenal have lost the first leg, also doing so in the 2008-09 Champions League against Manchester United (from which they were eliminated).
- Villarreal have progressed from 15 of their 16 two-legged ties in major European competition when winning the first leg - the only exception was in the 2015-16 Europa League semi-final, when they went out to Liverpool.
- This was the first time a former Arsenal manager (Unai Emery) had beaten the Gunners since George Graham's Tottenham side won 2-1 at White Hart Lane in a Premier League encounter in November 1999.
- Arsenal's Nicolas Pepe has been involved in more goals in Europa League this season than any other player (10 - 6 goals, 4 assists).
- Gerard Moreno has scored or assisted a goal in all seven of his Europa League starts for Villarreal this season, with the Spaniard setting up the second goal this evening.
- Arsenal's Dani Ceballos picked up his first red card in all competitions for a team playing in the top five European leagues (201st game).
The second leg of this semi-final will be played at the Emirates Stadium on Thursday of next week but before that, Arsenal face Newcastle in the Premier League, live on Sky Sports from 1.30pm on Sunday (kick-off 2pm), while Villarreal take on Getafe in La Liga on the same day.