Banyana nevertheless restored some pride after their 4-1 defeat to Sweden in the tournament opener and their 3-0 loss to Canada in their second match.
While the Japanese fielded a weakened side, Banyana did well to hold the world champions to a goalless draw.
Banyana coach Joseph Mkhonza said the Olympics had been a good learning curve for his side, who are ranked 61st in the world, while their opponents were all ranked in the top 10.
"It is a learning experience and it has put us in good stead for the future," Mkhonza said.
"The Olympics is the ultimate. There are thousands of footballers who wish to take part but only a few get the chance."
Midfielder Kylie Louw said the South Africans were playing for pride against Japan and had hoped to prove their worth.
"We had nothing to lose," Louw said.
"We have worked so hard just to qualify so we wanted to show our country that we can compete.
"A draw against the world champions is very exciting for us."
The Japanese took some shine off Banyana's heroics with revelations that the team was instructed to manufacture a draw.
"It was the coach's instruction that we wanted to stay in Cardiff and come second in the group," said Japanese player Azusa Iwashimizu.
"So I knew that the bench was getting information about the other match [Sweden v Canada] and I had been told."
Nonetheless, Banyana skipper Amanda Dlamini said her team's plans to hold off Japan had paid dividends.
"It was a good result," Dlamini said.
"At least we had a good plan to stick by and we contained the Japanese well." – Sapa