After a hard-fought opening draw with Mexico, the South Africans had their work cut out for them as early as the fourth minute.
Haruka Osawa made the most from poor defending to finish into an empty net to give the Japanese an early lead.
Following the set back, Bantwana tried to get back but were suffering with the drowning affect in the sweltering Maldonado heat.
Japan made it two after 23 minutes when Tanaka Tomoko capitalised on a loose ball for an easy finish into an empty net.
Bantwana were trying their best but the experience of the counterparts made ultra-hard for them to even conjure up any offensive movement.
Japan were handed a penalty and a chance to add a third after a foul inside the box. Tomoko stepped forward and blazed the roof of the net with a thumping finish.
Captain Sara Ito found time and space in the box to tuck away the fourth which deflected off a defender before finding the net.
Danger woman Osawa closed in on a second, but from close range blazed the stands instead of the back of the net a minute to halftime.
The Samarai were awarded another penalty after a foul by goalkeeper Kay-dee Windvogel. Ito made no mistake with a hard and low finish for her second of the day.
Bantwana threatened to slightly reduce the lead, but after being isolated for much the game, Chelsea Daniels failed to make the most of a half-chance in the closing stages.
Simphiwe Dludlu’s side were charging down for a consolation and finished strongly, but weren’t able to make the most of their few chances in around goal.
In added time, Yuzuki Yanamoto made it six following a cross-field delivery from Tanaka for an easy tap-in and comfortable victory.