The Japanese world number three was due to face Australia's Ash Barty later in the day and her place in the tournament will now be taken by alternate Kiki Bertens of the Netherlands.
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"I'm disappointed to have to withdraw from the Finals,” Osaka said.
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It has been a great event in Shenzhen, and it's the biggest WTA event of the year. This is not how I wanted to end this tournament or my season.
"I look forward to getting healthy and hope to be back here in Shenzhen next year."
Osaka won her first match of the tournament against Petra Kvitova of the Czech Republic 7-6(1) 4-6 6-4 on Sunday.
"It's not ideal," added Osaka, who lost all of her matches on her debut in Singapore 12 months ago.
"This is the second time I had to withdraw from the finals. I mean, the last time I at least played, so a retirement instead of a withdrawal.
"It kind of sucks because I thought I was playing well. I definitely wanted to win here."
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