Kuznetsova, seeded fifth, rallied from a set down for a 2-6, 7-5, 7-5 win in a quarterfinal that lasted 2 hours, 26 minutes at Ariake Colosseum.
Kuznetsova took a 6-5 lead in the deciding set when she broke Jankovic for the fourth time.
The Russian took a 40-30 lead with a smash at the net and then won the match on a drop shot that Jankovic couldn't reach.
It was a disappointing loss for Jankovic, who had been hoping to reclaim the world's top ranking with a tournament victory. The Serb struggled on serve with eight double faults.
Kuznetsova will next face the winner of the quarterfinal match between Olympic gold medalist Elena Dementieva of Russia and Slovenia's Katarina Srebotnik.
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