Zheng beat top seed Paula Badosa and fourth seed Veronika Kudermetova en route to her first WTA final.
However, the 19-year-old was undone by Samsonova, who has now won 18 of her last 19 matches, claiming three titles in that run.
Her 7-5 7-5 success in Tokyo made it two successive titles won without dropping a set and will move her up to a career-high ranking of 23.
Zheng, meanwhile, will become the first Chinese teenager to be ranked in the top 30. She is set to move up to 28th in the world.
"It was a really tough match because huge congrats to Qinwen and her team because she's playing amazing," Samsonova said afterwards.
"Seriously, congrats guys. It was a nervous match today. We were fighting every point. It was tough."