Matsuyama beat compatriot Hiroshi Iwata (63) on the first hole of a sudden-death playoff to capture his sixth career title on the Japan Tour, and fifth since April 2013.
Spieth, who closed with 69, finished one shot back, along with Australian Brendan Jones.
After a rollicking start, Spieth had been relatively quiet this summer. He recorded only one top 10 in an 11-event stretch before a T-8 at the limited-field BMW Championship and a spirited performance at the Ryder Cup.
The 21-year-old tied for 35th in the WGC-HSBC Champions, returned home to Texas and then finished joint third here in his first trip to Japan. He will join Rory McIlroy and Adam Scott in the field for next week’s Australian Open before closing out his year at Tiger Woods’ Hero World Challenge.
Matsuyama, meanwhile, won the Memorial in June and got his 2014-15 season off to a strong start, with back-to-back top 10s at the Frys and Shriners.