The Gunners endured a disastrous start at the Estadio de la Ceramica, falling behind inside five minutes as Manu Trigueros drilled a low shot into the far corner of Bernd Leno’s goal.
That early misery was compounded soon afterwards as Gerard Moreno’s flicked header was turned in at the back post by veteran centre-back Raul Albiol.
But as the tie appeared to be slipping away, with Dani Ceballos receiving a second yellow card early in the second half, Arsenal showed their resolve as Bukayo Saka won a penalty that was converted by Nicolas Pepe.
Pierre-Emerick Aubameyang came off the bench after Etienne Capoue was sent off for Villarreal but failed to convert a brilliant opportunity as Arsenal attempted to snatch a draw in the dying stages.
Under the circumstances, Arteta said he was pleased to see his side keep their hopes of reaching the final alive. “We didn’t want to come here and lose but after the way the game developed, you have to take the result. If you have to lose it is probably the best result we could have,” he said.
“Two different halves. We started to be us, in the first half there were so many moments we weren’t. We started to chase and were not precise with the ball, didn’t have enough control. We didn’t have enough threat or desire to attack the box, in the second half it was completely different.
“We are very used to that (Bukayo Saka playing well) this season, but it tells us we need to do much more as we cannot always rely on him. Bernd Leno was very good, at 2-0, the chance with Gerard Moreno, he saved us. We had a big chance with Auba to draw the game. I am confident we have a chance to win.”
Saka, who was once again his side’s standout performer, believed Arsenal will take plenty of confidence into the second leg after their much-improved display after the break.
“There’s a lot of positives which all came in the second half,” he said. “To start the game like that makes it impossible to have a chance of scoring. It’s really frustrating but I’m happy we picked ourselves up and managed to score.”