Bruno Duarte’s acrobatic equaliser ensured Arsenal had to settle for a 1-1 draw against Vitoria Guimares.
Shkodran Mustafi’s late header looked to seal the uneventful win - and all-but confirm qualification out of the group - for Unai Emery’s men with just ten minutes remaining.
But deep into stoppage time, Duarte converted to ensure the hosts took a share of the spoils in Portugal.
In doing so, he ended the Gunners’ perfect start to Group F in the Europa League and added unnecessary headaches for the Spaniard.
Emery’s men made eight changes to the team that drew at home to Wolves on Saturday, as Granit Xhaka was stripped of the captain’s armband.
But in a peculiar start, Vitoria’s Pedro Figueiredo Rodrigues, known also as Pepe, almost gave the hosts a shock lead when he struck a thunderous effort from range - only for it to rebound back off the bar.
Marcus Edwards was next to try his luck as Arsenal weathered an early storm at the Emirates, but Emiliano Martinez was equal to it.
Rob Holding, captain for the night in Pierre-Emerick Aubameyang’s absence, headed over from a good position midway through the first half, as the Gunners sought to take a lead against the run of play.
Davidson da Luz Pereira then struck wide as the hosts mustered up eight shots in the opening half hour, compared to the visitors’ one.
It was Frederico Venancio, though, who was left ruing the best chance of the half as the defender headed over from close range.
In a low-key start to the second half, Mustafi headed over from a corner-kick but visiting fans were left more concerned by the knock picked up by Dani Ceballos - who was substituted off in the 55th minute with an apparent hamstring problem.
Joe Willock hammered an effort well over the bar as Arsenal continued to miss the target, but they finally took advantage with just ten minutes remaining.
German defender Mustafi headed Pepe’s free kick back across goal and into the far corner as Arsenal thought they had stolen the win.
But former Tottenham forward Marcus Edwards was instrumental in ensuring the hosts shared the spoils, after his strong run forward saw a cross fall to Duarte, who stuck in the dying embers to salvage a point.
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