Tercious Malepe was given the captain's armband by David Notoane and lined up in a back three with Thendo Mukumela and Luke Fleurs, while Reeve Frosler started on the right flank.
The Japanese enjoyed most of the possession in the early stages of the encounter and had the South Africans pinned back in their own, although they only managed to register one effort on target in the opening 15 minutes.
Japan nearly got their opener when Koji Miyoshi pounced on a poor clearance to break through on goal in the 30th minute, but goalkeeper Ronwen Williams rushed off his line to thwart the attacker.
While South Africa provided no attacking threat throughout the half, Japan did have the ball in the back of the net through Daichi Hayashi in the final 10 minutes, but the strike was ruled out for an offside.
Japan continued from where they left off in the first half and they should've been ahead 10 minutes into the second stanza, but Hayashi failed to beat Williams from six-yards out.
Japan coach Haijme Moriyasu opted for his first change on the hour mark, with Miyoshi making way for Yuki Soma while Notoane seemingly had no plans to refresh his stall.
After waves of attack, South Africa's resistance was eventually broken on 70 minutes when Takefusa Kubo found the bottom corner with a powerful strike that left Williams with no chance.
Notoane's charges managed to carve out a glorious chance for Thabo Cele seven minutes later but the midfielder, who had time and space, fired straight the Japanese goalkeeper.
Kobamelo Kodisang and Nkosingiphile Ngcobo were introduces in the closing stages of the half as South Africa went in search of an equaliser, but Japan managed to hold out until the final whistle to claim maximum points.
South Africa: Williams, Malepe, Fleurs, Mukumela, Frosler, Mosele, Mokoena, Mabiliso, Singh, Cele, Makgopa.
Subs: Mpoto, Mlungwana, Mahlangu, Mohamme, Ngcobo, Kodisang.