Spain and Croatia went into the last 16, but not in the order expected. Euro 2016 has another late goal and this is one whose impact may prove enormous, the holders suffering their first European Championship defeat for 12 years and a day. With the score at 1-1 and 87 minutes gone in Bordeaux, Aritz Aduriz’s shot was blocked on the edge of the area; two passes and 80 yards later, Ivan Perisic was tearing off his top and Croatia, not Spain, were top of Group D.

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Croatia will face a third-placed side in Lens; Spain will play Italy in Paris, knowing that Germany and then France may await. “This is just the beginning,” Perisic said, while his coach, Ante Cacic, talked of confidence and the need to “make the Croatian people happy”. That the chances of one of the competition’s outstanding sides are improved now was revealed by his opposite number. “This was not the path we wanted, that’s the truth,” Vicente del Bosque admitted.

If Spain are to defend their title, they must do it the hard way and they cannot say they were not warned: Sergio Ramos had a second-half penalty saved by Danijel Subasic that might have made it safe but the threat had been there since Nikola Kalinic levelled at the end of the first half. When that went in, this changed. When the winner did, the group changed too. The whole tournament did, in fact.

Aduriz was denied and two swift diagonal passes from the back gave Perisic, superb throughout and still sprinting up the field now, a sight of goal. Perisic had made the first for Kalinic; this time the roles were reversed. The shot clipped Gerard Piqué’s boot and flew in at the near post beyond David de Gea who, falling backwards, had tried to stop it with his foot.

Behind De Gea the Croatian fans erupted. The goalkeeper was edgy for much of the match and there will be questions about him and not just on the winner, however much his manager said he was not to be blamed. Spain’s fans were silent at the end of a night in which it felt as if the team had not entirely grasped the game’s significance until it was slipping away. “A lapse in the 89th [sic] minute with the score in our favour is not something we should allow to happen,” Del Bosque said. “We have to recover mentally and emotionally but we’re still here.”

As for Caric’s team, they may consider themselves candidates now: they had beaten Spain without Luka Modric and despite trailing after six minutes. That goal, like the winner, 81 minutes later, came via a move in which the ball travelled virtually the length of the pitch, until David Silva found Cesc Fàbregas and his clip over Subasic was nudged in on the line by Álvaro Morata.

If the chance to finish third rather than second as a way of avoiding Italy, Germany and France really was on Croatian minds, the idea was dismissed a moment later with news that Turkey led. Better, then, to step out. And soon they were almost level. Under pressure from Kalinic, De Gea’s dreadful clearance dropped to Ivan Rakitic, whose first-time, curling lob was beautifully struck only to hit the bar, the post and the goalline. Rakitic looked at the giant screens, as if trying to work out how on earth it had not gone in.

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If that would have been a lovely goal, the one Croatia did get on the stroke of half-time might have been better still, Perisic turning away from Juanfran and dropping a delightful cross into the six-yard box. Ramos was beaten to it, De Gea did not move and Kalinic jumped to ease in a gentle, back-heel-style volley with the outside of his foot. Until then this had been an open, entertaining game, if seemingly lacking in the tension and concentration of a decisive match. It had also been mostly controlled by Spain, whose axis had tilted from left to right, from Andrés Iniesta and Nolito to Fàbregas and Silva.

The Manchester City playmaker shone but Spain not only failed to increase their lead, they lost it. Kalinic’s goal was the first they had conceded in 733 European Championship minutes, stretching back to the opening game against Italy four years ago. And although the second half started with a chance for Morata, the Croatian threat was clearer now; Perisic, fast feet, determined to run at opponents, was especially troubling.

His run led to the Darijo Srna cross that had De Gea scrambling and star-jumping, the ball eventually flashing wide from Marko Pjaca’s overhead kick, and then Pjaca went over Ramos’s leg. Ramos accused him of diving and may have been right but there was risk in the challenge. The referee did not give that but did give one at the other end when Sime Vrsaljko was judged to have pushed Silva. The contact was slight at most and accidental too, the defender stumbling, possibly pushed. Yet the Croatians’ fury became celebration when Subasic, dancing about, lurched forward to save the penalty, struck centrally by Ramos – an unexpected choice of taker and one Del Bosque justified as a question of “confidence”.

Gerard Piqué prevented Kalinic running through and Spain sought the winner to set them up for the fortnight ahead, but just how costly that miss was became revealed when Croatia broke with three minutes to go to turn the table and the tournament upside down.