Jones' final round of 8 under 64 was the best of the day and moved him from a share of 21st to a tie for 2nd place with Ryo Ishikawa, Kyung Tae Kim and Ryuko Tokimatsu.
The Canberra native was unable to pick up one extra birdie over the closing stages to force his way into what would have been a playoff but will jump to 28th on the Japan Tour money list for 2017 with earnings over $400,000.
The winner of the event was American Seungsu Han who won his first Japan Tour title.
Brad Kennedy was the next best of the Australians, finishing in a share of 12th.
Kennedy and Jones will be joined by Todd Sinnott as the only Australians at the season-ending Golf Nippon Series event in Tokyo this week.
JUSTIN ROSE: REFLECTIONS ON 2017
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