The Asian nation defied the odds to top Group E on Thursday night as they beat Spain 2-1 following a stunning second-half comeback.
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In doing so, they knocked out Germany despite Hansi Flick's side winning 4-2 against Costa Rica.
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Germany needed to win their final group match, while hoping Japan suffered a defeat to Spain.
And the signs were positive for Germany at half-time as Spain led 1-0, only for Japan to turn the game on its head within six minutes of the restart thanks to goals from Ritsu Doan and Ao Tanaka.
Japan then survived an onslaught of pressure from Spain, and though they had just 17.7 per cent of possession, they held out for a famous win.
But despite the euphoria inside the Khalifa International Stadium, Samarai Blue supporters put their celebrations on hold.
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In what has become synonymous with Japan fans after matches, those in the stands tidied up to leave no trace of littler on the floor.
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Fans were caught on camera with plastic bags as they went round the stadium filling it up with rubbish.
Social media was loving their act of selfless kindness, as one user tweeted: "Japan deserve to qualify not only have their fans shown service to humanity by always cleaning the stadium but also show great strength."
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Another quipped: "Japan fans should go and collect bags full of tears in the stadium where Germany played."
A third added: "Huge respects for the Japanese fans in Qatar, what they did is just speechless & amazing!"
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Japan players have showed just as much respect this tournament, with a picture of their spotless dressing room after their opening group win over Germany going viral.
talkSPORT's Ally McCoist was full of praise for Japan, as he said: "I don't know if you've heard or seen the story of the Japanese players and staff cleaning up the dressing room, they left it absolutely meticulously clean.
"As if that wasn't enough, there's footage going about of Japanese fans going about with bin bags even after the games.
"I've got to say that's my story of the day, it's absolutely brilliant."
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