The Australian, ranked No.94 in the world, had been impressive in earlier wins over sixth-seeded Romanian Sorana Cirstea and Spain's Cristina Bucsa to book her spot in the quarter-finals at the WTA 500 event against Kamilla Rakhimova.
The Uzbekistani won a tight first set 7-5, before Joint rebounded to claim the second by the same scoreline.
However, Â Rakhimova romped away in the final set to win 7-5 5-7 6-1 in Tokyo on Friday.
Joint took the honours when it came to the first serve, landing 66 per cent compared with her opponent's 59 per cent, as well as serving five aces to just one from Rakhimova.
However, world No.66 was much more effective on her return, converting six of the 12 break points she set up, compared with the three breaks Joint managed.
Despite the loss, the late-season Asian swing has been a welcome confidence boost for Joint.
Ranked a career-high No.28 in February, the Australian's year had been underwhelming until she made the final at last month's Korea Open in Seoul, where she lost to compatriot Kim Birrell.
The signs are certainly promising for the 20-year-old as she plans her assault on the Australian Open in January.
Rakhimova's victory set up a semi-final against Leylah Fernandez.
The Canadian was given an armchair ride into the semis when world No.1 and reigning Australian and US Open champion Rybakina withdrew from their quarter-final because of injury.
Rybakina said she could not play because of an undisclosed injury. She stood on the court in Tokyo and delivered the news to fans and ended by saying "I hope to see you all next year."
She said she had been struggling for several day "with a little injury" and needs to be ready for next month's WTA Finals in Indian Wells, California.
Rybakina ensured she will be ranked No.1 at the end of the year with Thursday's victory over countrywoman Yulia Putintseva.
Also on Friday, Slovenia's Mia Pohankova beat American Alycia Parks 7-6 (7-3) 6-3 in their quarter-final.
Pohankova turned 18 last week and was a wildcard entry in the tournament.
In the late quarter-final, No.3 seed Diana Shnaider, of Russia, fought back to claim a 2-6 7-6 (7-4) 6-4 win over Alexandra Eala, the eighth seed from the Philippines.
Shnaider's victory set up a semi-final against Pohankova, who is looking for her first WTA title.
- With The AP
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