Currently just outside the eight qualifying spots for next month's WTA Finals in Singapore, Pliskova has now spent 420 minutes on court in Tokyo compared to 222 minutes for Osaka.
The Czech former world number one came into the contest having spent 419 minutes on court this week, more than any other player despite a first round bye and nearly twice as long as Osaka.
Third-seed Osaka, 20, said after the match that she "felt really exhausted today" and that she "wasn't doing the little things well", after having not dropped a set in tournament until Sunday.
Pliskova broke Osaka for a second time to go up 5-4 in the second set and then hammered her sixth ace to secure her 11th career title.
Pliskova needed three dramatic sets in each of her matches to reach her second final of the season.
Naomi Osaka continued her winning streak with another comfortable victory to move into a Tokyo Open final clash against Karolina Pliskova.
The Dutch second seed rallied after losing the opening two games of the decisive set, eventually winning 7-6 (2) 4-6 6-2 in two hours and 22 minutes.
"The chances of me playing in the next tournament are very low".
"I have literally never been so exhausted in my entire life", she told reporters.
When asked to explain her lackluster performance, Osaka replied: "If I know I would have fixed it".
The Japanese third seed, who was hoping to go a step further after reaching the final in 2016, began in menacing fashion.
The third set was tight with a break of serve coming early for Pliskova in the third game to lead 2-1.
"Also confidence gets higher and higher with every match that you win and I won a lot of tough matches here, a lot of tough sets against tough opponents, so I'm proud of this".
"She has basically every shot and she has a really good serve, so I know it will be a very hard match".
Reigning US Open champion Naomi Osaka of Japan withdrew from the Wuhan Open on Sunday due to a viral illness. That's normal in semifinals - there's no easy opponents."I think Donna was playing well and she's beaten a lot of tough players this tournament".