In the light of day Arsenal will not be too hard on themselves, and nor should they be. Elimination from the Europa League to a commendable Sporting side will hardly register as a regret if Mikel Arteta’s players use a cleared schedule to succeed in their push for domestic glory. Nonetheless the novelty of seeing late drama work in an opponent’s favour was unwelcome and a night that stretched to the bitter end may yet have further unwelcome consequences.

Nuno Santos’s emphatic penalty, settling a shootout that had tilted Sporting’s way when Antonio Adán repelled the previous kick from Gabriel Martinelli, sparked delirious scenes among the green and white-clad away contingent. Large numbers of the home support stayed to chant defiantly, aware that this surprise setback should not dampen anything that has passed before. Arsenal did not quite deserve to go through over the two legs but would have still navigated extra time successfully had Adán not saved magnificently from Leandro Trossard and Gabriel Magalhães; the fine margins cannot go your way every time.

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The real pain may be physical rather than emotional. Arsenal took some almighty blows here, even though Sporting’s challenges were generally fairly contested until Manuel Ugarte was shown a second yellow card for clattering Bukayo Saka at the very end. They lost Takehiro Tomiyasu and, more inconveniently, William Saliba to injuries inside the first 21 minutes while Gabriel and Aaron Ramsdale were among those to need treatment during the game. Trossard and Oleksandr Zinchenko also appeared to pick up knocks. These were consequences of a tense, bruising, engaging cup tie but Arsenal cannot afford to lose first-teamers for their title drive.

“Tomiyasu looks pretty serious, from his reaction straightaway and what he said to me,” Arteta said. The right-back had appeared to overstretch after being left for dead by Francisco Trincão early on. He was less clear about the significance of Saliba’s ailment, which saw him replaced straight after Granit Xhaka had given Arsenal the lead, but losing the Frenchman for any length of time would be a sizeable blow.

In his absence Arsenal were unconvincing at the back although it did not help that the defence was exposed by a negligent midfield. Sporting had shown flickers of danger in the first half and begun the second period strongly when they punished Granit Xhaka and Jorginho for overplaying near halfway, although nobody could have predicted the consequence of their laxness. Pedro Gonçalves was six yards inside Arsenal’s half when, from nothing, he elected to shoot and caught Aaron Ramsdale off his line. The ball sailed over his head and in; it was a stunning goal and Arsenal, who had refused to turn the screw, had it coming to them.

“A huge blow,” Arteta said of the disappointment that followed. “We really wanted to go through, fight and go for it. We tried for 120 minutes and it wasn’t enough.” For the final hour Arteta fielded his first choice front six, assuming Trossard is part of that for now, but while they stemmed Sporting’s flow they rarely clicked. Trossard should have won it when Dário Essugo’s disastrous backpass sent him through but Adán diverted on to a post; Gabriel was agonisingly close with two headers at the death, one cleared off the line, but when you court jeopardy so often it will not always fall for you.

Arteta will simply be relieved if Ramsdale, who took a whack to the face when denying Marcus Edwards a winner late in normal time, and his hobbling colleagues are fit to face Crystal Palace on Sunday. A straightforward evening’s work had seemed likely when Xhaka swept in emphatically after Martinelli, sent away beautifully by Jorginho, had shot too close to Adán. Sporting had started with intent but did not appear especially equipped to come back until grasping that Arsenal were a shadow of their usual intense selves.

The good news came in the form of a successful full comeback for Gabriel Jesus, who started for the first time since returning from injury and departed at half-time as planned. Jesus looked sharp enough and almost doubled the lead when, after twisting into space, his angled drive was stopped by the inspired Adán. His availability will look especially timely if Arsenal’s collateral damage transpires to have been heavy.

Arteta’s task is to ensure confidence does not take a hit and he said Martinelli, disconsolate at the end, would “react well” to his fluffed penalty. Clear heads may be able to take advantage of free midweeks over the next two months. “The disappointment is not going to go away,” he said. “But there’s also a clarity. There are 11 games to go and we have a final against Palace.” Win that, and the impossibility of a May showpiece in Budapest will feel all the more palatable.