Sakamoto leads skating swansong with 'Time to Say Goodbye' at worlds
In the absence of reigning Olympic champion Alysa Liu, the silver medallist at Milan Sakamoto scored 79.31 points.
Chiba was a whisker behind on 78.45, while the American Amber Glenn was third on 72.65.
The free programme is scheduled for Friday, where the 25-year-old Sakamoto hopes to bid farewell on a winning note on what she says will be her final professional outing.
"I had high expectations for the Olympics, and many people around me expected a lot from me as well. Not being able to meet those expectations was therefore very, very sad for myself," Sakamoto said.
"But a week before I arrived here, I started delivering clean, error-free programmes every day in training. So I think today's performance reflects what I am capable of."
On Wednesday, her performance to the aptly named "Time to Say Goodbye" by Andrea Bocelli earned her her best score of the season, while Chiba also took a season's best, skating to the disco sounds of Donna Summer.
By contrast, the third Japanese skater in contention, Ami Nakai, bronze medallist in Milan, missed her opening triple Axel and dropped to eighth place.
With 69.10 points, however, she remains in the race for a podium finish.
The competition continues later Wednesday with the pairs short programme.