Rybakina received a bye into the last 16 of the WTA 500 event in Tokyo and arrived at the Ariake Coliseum after capturing her fourth title of the season and first as the top-ranked player at last week's Ningbo Open in China.
The 27-year-old, who rose to world number one for the first time en route to winning the US Open last month, needed only one more victory this year to ensure that world number two Aryna Sabalenka could not overtake her.
Rybakina is enjoying a marquee year with wins at the Australian Open and US Open to take her Grand Slam tally to three, after winning Wimbledon four years ago.
"It means a lot, this is something we worked for with the team," said Rybakina.
"So many great players and we are all really close to each other, and I'm happy that now with last week and with today's win I made it possible to secure number one at the end of the year.
"It's an amazing achievement and hopefully we can continue this way next year," she added.
She next faces Leylah Fernandez in a rematch of their Ningbo final, after the Canadian beat Elise Mertens 6-2, 7-6(8).
Rybakina endured a brief dip after her US Open triumph, losing her opening match in Beijing and missing the Wuhan Open due to a leg injury, before defending her title in Ningbo.
She is targeting a 16th career title before heading to Indian Wells, California, for the WTA Finals, where the season's top eight players will compete from November 8th-15th.
"Today the serve definitely helped me in the important moments," Rybakina said.
"I was just trying to pick my spot and I think today with a closed roof and a combination of the balls and the court made me feel better serving.
"I'm glad today it worked."