Fifth-seeded Kuznetsova rallied from a set down for a 2-6, 7-5, 7-5 win in 2 hours, 26 minutes at Ariake Colosseum.
The Russian took a 6-5 lead in the deciding set when she broke Jankovic for the fourth time. Kuznetsova went 40-30 ahead with a smash at the net and then won the match on a drop shot that Jankovic couldn't reach.
"I knew I had to be more aggressive in the third set,'' Kuznetsova said. "If you don't take a risk, you don't drink champagne.''
It was a disappointing loss for Jankovic, who had been hoping to reclaim the No.1 ranking from Serena Williams with a tournament victory. The Serb struggled on serve with eight double faults.
"I played well in the first set and then my percentage of serves started getting lower and lower,'' Jankovic said. "I made double faults at the wrong time and lost my serve many times and that was the key.''
Jankovic lost to Serena Williams in the final of the U.S. Open.
"Coming off the U.S. Open it's hard to be at the top of your game,'' Jankovic said. "I have five tournaments left this year and still have a chance to finish at the top of the rankings and that's the most important thing to me.''
Kuznetsova will face qualifier Katarina Srebotnik of Slovenia in the semifinals on Saturday.
Srebotnik upset Olympic gold medalist and third-seeded Elena Dementieva 6-3, 6-4.
Russia's Nadia Petrova also advanced to the semifinals with a 6-3, 6-0 win over sixth-seeded Agnieszka Radwanska of Poland and will face compatriot Dinara Safina on Saturday.
Fourth-seeded Safina ousted Kaia Kanepi of Estonia 6-4, 6-7 (5), 6-2.
Kuznetsova downs Jankovic at Pan Pacific Open
Jankovic advances to Pan Pacific Open quarters
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