The four-times Olympian, 39, headed to Japan with a clean bill of health and was confident that her third career race over 26.2 miles would be her best yet.
However Pavey failed to finish, with 35-year-old Lydia Cheromei of Kenya coming home first in 2:23:07.
Pavey clocked 2:28.24 at the London Marathon last year before posting 2:28.42 in New York and took to Twitter to express her utter disappointment.
"Feel mortified. In nearly 30 years of racing that's only the 2nd time I have stopped in a race. Last time was Euro Indoors when calf tore," she said.
"Really disappointed. Perfect preparation & then had sore throat since Thursday night. Running can be so frustrating. Could not finish today."