This was a lesson Arsenal had to learn eventually but it could not have come at a more costly moment. Pierre-Emerick Aubameyang has spent two years bailing out sluggish performances and embodying a model of consistency in a team that has shown none. He seemed to have done it yet again, with the stakes perhaps higher than ever, when he arched his back and cracked in a breathtaking overhead volley seven minutes from the end of extra time, restoring their aggregate lead with his first significant involvement of the game. But then came two stark, devastating reminders that Mikel Arteta’s rebuilding job has barely scratched the surface.

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Olympiakos would, on this showing, have been unfortunate not to reach the last 16 and they received one last chance to load the Arsenal box when Bernd Leno conceded a corner under little pressure. There followed an object lesson, and not the night’s first, in how not to defend after a set piece: although the initial cross was cut out by Gabriel Martinelli, he could not get out quickly enough to prevent Giorgos Masouras having another go and from there the die was cast. Masouras’s inswinging, left-foot delivery was good enough to ask questions and the response was, from an Arsenal perspective, nonexistent. David Luiz watched the ball float in front of him as if oblivious to the danger that lay behind, where a flat-footed Sokratis Papastathopoulos had given Youssef El Arabi space to stab in from six yards and spark a mini pitch invasion from the visiting staff.

You can have all the world-class strikers on the planet, but you cannot legislate for a backline that falls far short of where Arteta requires Arsenal to be. Unfortunately you cannot legislate for those rare moments when your centre-forward malfunctions, either. El Arabi’s goal had come with a minute to play but, incredibly, there remained time for Aubameyang to contrive an improbable miss. A ricochet found him alone in front of goal but, beyond every expectation, he blasted wide; there was to be no saviour act after all but no blame ought to linger his way.

Facebook Twitter Pinterest Pierre-Emerick Aubameyang reacts to his last-gasp miss. Photograph: Chloe Knott - Danehouse/Getty Images

“I feel very, very bad,” a desolate Aubameyang said afterwards. “But it can happen. I don’t know how I missed this chance.” He deserved credit for facing the cameras but this outcome, which removes a huge chunk of meaning from Arsenal’s season, cannot be pinned on him. They had done the hard part, or so it seemed, by winning in Piraeus and should have been able to complete the job against opponents who do not travel well. Arteta had picked a full-strength team in a clear indication of the night’s importance: Arsenal need to be in the Champions League and a sensible performance would have greatly improved their prospects of getting there via this competition.

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They started too slowly, barely creating a chance in the first 45 minutes.

While Olympiakos were little better, they could point to a miss by Abdoulaye Camara that set alarm bells ringing and the sense, at half-time, was that Arsenal had thrown them a bone. Arteta has drilled shape and structure into what is essentially a mediocre bunch; of that there is no doubt. But they are not good enough to offer practised opposition this much of a sniff and, when Mathieu Valbuena swirled over a 53rd-minute corner, the point was underscored. Pape Abou Cissé, given a clear run on to the ball as it sailed over Shkodran Mustafi, nodded it past Leno and from that moment Arsenal were walking on eggshells.

Quick guide Roundup: Inter see off Ludogorets at empty San Siro Show Hide Internazionale came from behind on the night to beat Ludogorets 2-1 at an eerily quiet San Siro, completing a 4-1 aggregate victory in a game played behind closed doors due to coronavirus fears. No fans were present at the 70,000-capacity stadium as a near-post finish from Cristiano Biraghi and a Romelu Lukaku header denied the Bulgarians, who had taken the lead through Cauly Souza.

"It seemed like a training session, playing behind closed doors created a very strange atmosphere," said Inter coach Antonio Conte. "The lads did well to put things back in place immediately after we suffered the goal."

It was a night to forget for Portuguese sides, with Benfica, Porto and Sporting all joining Braga in going out at the last-32 stage. Benfica drew 3-3 with Shakhtar Donetsk in Lisbon, losing 5-4 overall, while Porto were outclassed by Leverkusen, who won 5-2 on aggregate. Sporting were twice within a minute of overcoming Istanbul Basaksehir, only for Edin Visca to score on both occasions – first to send the game into extra time, and then to complete a 5-4 aggregate win from the penalty spot. Jaime Mata's early goal for Getafe made the difference as they edged out Ajax despite a 2-1 defeat in Amsterdam. Elsewhere, Justin Kluivert cancelled out Jonathan David's opener as Roma progressed with a 1-1 draw at Gent, while Sevilla were held to a 0-0 draw by Cluj, but edged through on away goals. Photograph: Emilio Andreoli/UEFA

There were moments when a happier outcome seemed possible, not least when the frustrating Nicolas Pépé’s effort was parried by José Sá, but Arteta’s post-match assertion that Arsenal had created enough chances felt like a mechanism for protecting his players. Olympiakos carried a constant threat on the break and, before the late drama took hold, could have found a winner when Masouras’s dipping effort clipped the bar. They had started the match tentatively but could not fail to detect the skittishness in Arsenal, which manifested itself in cheap concessions across their entire team. It had been hard to identify a major weapon in Pedro Martins’ side during the first leg but they grew in stature here, too often reducing Arsenal to a scurrying, confused unit more reminiscent of Unai Emery’s latter days.

Facebook Twitter Pinterest Youssef El Arabi celebrates after scoring in the last minute of extra time. Photograph: Adrian Dennis/AFP via Getty Images

Perhaps things would have been different if Mustafi’s 103rd-minute departure through injury had not disrupted Arsenal’s defence; Papastathopoulos looked well off the pace in his cameo. But ultimately this was a night of huff and puff, with too much onus on one man to blow the house down. Arteta believes Aubameyang is keen to stay at Arsenal beyond the end of his contract, which expires next summer, but he will want to offer his star turn a seat at the top table. Their best chance to take one may have evaporated and the consequences could yet be far-reaching.