As Kenya's Catherine Ndereba claimed marathon gold on the final day of the World Championships in Japan.
Yamauchi, who lives in Japan, was in contention with just six miles to go but then fell away to finish in two hours 32 minutes and 55 seconds.
Ndereba broke clear in the last two miles to beat China's Chunxiu Zhou and Japan's Reiko Tosa in 2:30.37.
Briton Paula Radcliffe did not defend her title because of a back injury.
Yamauchi succeeded in reducing the leading pack from 20 to nine with an injection of pace at the 18-mile mark.
I thought this is my big chance so I've got to try, but I died a bit after that
Mara Yamauchi
But the 34-year-old soon got overtaken by her more experienced rivals, and finished in ninth - an improvement on her 18th-place finish in Helsinki.
"The men's race was decided right at the end so I thought I had to keep something in reserve," said Yamauchi.
"I thought this is my big chance so I've got to try, but I died a bit after that."

Britain's Tracey Morris, who is on the comeback trail after knee surgery, finished 19th in 2:36.40.
"I tried to put it all into this one day," said Morris, who finished comfortably.
There are seven more finals to be decided on the final day of competition in Osaka in the women's high jump, 1500m, the men's 5,000m, javelin and 800m and the 4x400m relays.