The win for the Samurai Blue ensured their progression and confirmed Germany's exit, while briefly putting Spain's qualification under threat for a few minutes.
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There was some confusion about the winning goal as Kaoru Mitoma's touchline cross looked like it had gone over the line and should've been ruled out, before Ao Tanaka prodded in.
There's been plenty of debate whether the goal have stood but now FIFA, 24 hours later, say the right decision was made.
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FIFA, in a series of tweets to clarify the situation and clear any confusion about the goal's legitimacy, said: "Japan's second goal in their 2-1 win over Spain was checked by VAR to determine if the ball had gone out of play.
"The video match officials used the goal line camera images to check if the ball was still partially on the line or not. Other cameras may offer misleading images but on the evidence available, the whole of the ball was not out of play."
The tweets were provided with video evidence and it's been proven that the ball was in play by 1.88 millimetres, which proved too be the difference between Japan's qualification to the last 16 and Germany suffering a second-straight group stage exit.
Japan are due to play Croatia next in the last 16 in the hope of reaching the quarter-finals while Spain take on Morocco, with both having narrowly missed out on a berth in the last eight in Russia four years ago.
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A day after the controversy, there was more as Uruguay will feel aggrieved not have been given at least one penalty in their final group game against Ghana.
Despite winning 2-0, they were eliminated on goal difference and furious players chased officials down the tunnel at full-time to make their point.