Needing some strong results on the Asian swing to force her way into next month's WTA Finals, Wozniacki reached the last four with a 6-2 2-6 6-3 win over Kerber, who had won three of their last four clashes.
"It was a tough match -- it always is when I play Angelique," said Wozniacki, who won the Tokyo event in 2010 and was runner-up last year.
"I started off well in the first set. I was playing well, and she was making quite a few errors. Second set it turned around, but it was competitive towards the end, and in the third set I thought we both played at a really high level."
Wozniacki's semi-final opponent will be Switzerland's Belinda Bencic, who defeated Garbine Muguruza of Spain 7-6 (1) 6-1.
The defending champion, Serbia's Ana Ivanovic, was knocked out in Friday's quarter-finals by Dominika Cibulkova, losing 7-6 (5) 6-3 to the Slovakian.
Cibulkova will play the 2011 Pan Pacific champion, Agnieszka Radwanska after the Pole overcame big-hitting Karolina Pliskova of the Czech Republic 7-5 6-2.
"My hands are a bit sore returning those 190km serves, but I'm good and ready for the next one," said Radwanska.
(Reporting by Julian Linden in Singapore; editing by Sudipto Ganguly)
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