Japan were clinical and made use of their chances and have now proceeded to the quarter-finals after the win against the Mzansi youngsters.
Meanwhile, the match started with a high tempo, and South Africa managed to test the Japanese in the seventh minute when Selwyn Stevens fired from just outside the box, but his shot was deflected out for a corner.
Neo Bohloko, who was a constant threat against the Japanese, came close to breaking the deadlock in the 15th minute when their opponents lost possession in their own half. However, the Kaizer Chiefs star sent his effort way off target when he only needed to calm down and fire from close range.
Another chance for the Africans came in the 17th minute when Emile Witbooi, after beating a number of Japanese, spotted Bohloko, but again, the Amakhosi youngster fired over the bar.
Mamelodi Sundowns' Lwandiso Radebe saved Amajimbos from going down in the 20th minute; the goalkeeper left his line and blocked an onrushing Shimon Kobayashi.
Japan made a change in the 21st minute after Simon Yu Mendy could not proceed. The Japanese youngster collided with Tumi Mothapo as they vied for an aerial ball. After both were attended by the medics, Mothapo returned to action, but Mendy was replaced by Shota Fuji.
Minutes after receiving medical attention, Mothapo made a match-saving block on Daigo Hirashima in the 22nd minute. Mothapo has been a sensational star for Amajimbos in the tournament, and how timely he blocked Japan's star from scoring is a testament to his top-level performance.
Amajimbos survived in the 38th minute when a free kick was delivered from the left flank into the area. Anthony Motosuna connected to it and headed only to be denied by the crossbar. Radebe blocked the rebound before the danger was finally cleared.
Radebe came to the rescue of South Africa once again when he quickly reacted to clear a low shot from outside the box. Despite the fact that he was partially blocked by the players in front of him, he was able to spot the ball and clear it away.
Shaun Els managed to create some shooting space for himself, but he was denied by the Japanese goalkeeper, who conceded a corner in the process in the 45th minute.
Eventually, Radebe was beaten when he conceded in the 47th minute when Hiroto Asada scored.
Despite making two quick back-to-back saves, the ball ended up getting into his net. The goalkeeper was, however, let down by his defenders, who just looked on and were slow to act and clear the danger.
After making saves that denied Japan goals, Radebe left the pitch in the 57th minute. Vela Khumalo replaced the starlet, who was injured in the process of trying to block Japan from scoring, with Keabetswe Morake.
Two minutes after Radebe left the pitch, South Africa conceded the second goal, scored by Minato Yoshida.
The Asians stretched the scoreline further when they found the back of the net through Fuji in the 72nd minute for their third goal.
Their determination against an equally hard-fighting opponent saw them grab the win and a clean sheet.

Although Amajimbos have exited the global competition, their undying spirit was visible for everyone to see. They head back home with their heads held high, although, back in their minds, it was their ambition to remain in Qatar and continue to fight for global glory.

They defeated Bolivia 1-0 in their first Group A game despite the fact that they were a man down.
Amajimbos were held by Qatar to a 1-1 draw and lost the final group game to Italy by a 3-1 margin.
Khumalo's charges managed to reach the knockout stage after finishing second in their group.