Yasmany Tomas opened the scoring with a long home run in the third inning and Alfredo Despaigne connected for a three-run blast in the eighth for Cuba, who clinched top seeding from Pool A in their showdown against the two-time defending champions.
Cuba, like Japan, were already assured of advancing to the second round in Tokyo after posting a 2-0 record, but the win was important to the Cubans, who lost to Japan in the 2006 final and twice to them during the second round in 2009.
"Tonight's win has a lot of meaning," Cuba manager Victor Mesa said through an interpreter after their win in Fukuoka, Japan. "We got a lot of confidence from that."
Cuba will begin the second round on Friday at the Tokyo Dome against the Netherlands. Japan will meet Pool B winner Taiwan in the modified double elimination phase of the championship.
Semi-finals and finals of the tournament will be played in San Francisco on March 17-19.
Cuba led 6-0 going into the ninth inning before Japan rallied for three runs.
The Japanese struggled at the plate for the third straight game, going 2-for-9 with runners in scoring position and stranding 10 men on base.
"Some of the hitters are in good condition, but some aren't," Japan manager Koji Yamamoto said.
In a bright spot for Japan, struggling ace Masahiro Tanaka looked good in a relief appearance, striking out six of the last seven batters he faced in two innings of work.
First-round play in the other two pools begins on Thursday with Venezuela meeting the Dominican Republic to launch Pool C in San Juan, Puerto Rico, while Italy and Mexico play in Phoenix, Arizona in Pool D.
The U.S. team play their first Pool D game on Friday against Mexico, and Canada open their tournament against Italy. Puerto Rico meet Spain in the other Pool C opener on Friday.