The organisation said the 55-year-old Australian, who has been the Brave Blossoms' coach since 2012, will resign on November 1. His contract was due to expire this year.
The decision was approved by the group's board of directors, with Jones also to quit as the director of rugby at Japan's new Super Rugby side.
A new coach will be chosen after the World Cup starting next month, when Japan will accelerate their preparations to host the tournament in 2019.
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