The Moscow-born Kazakh was due to face Canada’s Leylah Fernandez in the quarter-finals, but instead she came onto the court to address the crowd and sign autographs.
She said she would return for next month’s WTA Finals in Indian Wells.
“I just wanted to say thank you so much for coming today, but unfortunately I won’t be able to play,” said the 27-year-old.
“I’ve been struggling for a couple of days with a little injury.
“It’s difficult for me to come and play at 100 percent since there is also a very important tournament coming up.”
Rybakina clinched the year-end top ranking with a 6-2, 6-3 win over Yulia Putintseva in her opening match in Tokyo.
She became world number one for the first time last month in winning the US Open, replacing Aryna Sabalenka at the summit.
The achievement capped a year in which Rybakina also won the Australian Open in January and now has three Grand Slam titles.
She arrived in Tokyo after winning her fourth title of the season last week at the Ningbo Open in China, beating Fernandez in the final.
“Thank you so much for all the support throughout the year, especially here in Tokyo,” she said.
“It’s an amazing city. I really enjoy it every time I come, but unfortunately this time I won’t be able to play.
“Thanks again and hope to see you all next year.”
