Bencic will now have another chance to win the trophy and erase bitter memories of her straight-sets defeat by Poland's Agnieszka Radwanska in the 2015 final, and the Swiss player said she was looking forward to the challenge.
"I'm really excited to be back in the final," Bencic said. "It's been a while ... 10 years, so I'm really happy."
Playing under the centre court roof of the Ariake Coliseum due to rain, both players stayed strong on serve in the opening 12 games before Swiss Bencic turned up the intensity in a tight tiebreak to take the opening set with a forehand winner.
Former Australian Open champion Kenin wiped the slate clean and came out firing to bag a break in the fourth game of the second set and overcame a minor wobble on her own delivery in the next game to eventually draw level in the contest.
'Difficult match'
Bencic, the Tokyo Olympics gold medallist, broke for a 3-1 lead in the decider after some sloppy play by Kenin, and the 28-year-old rode the momentum to wrap up the victory and stay on course for her second title of the season.
"I think it was a very difficult match," said Bencic, who won the Abu Dhabi title in February, four months after returning to the circuit from maternity leave.
"I'm really exhausted at this point. I tried to shorten the points, take more risks and tried to go for it. Thankfully today it went my way."
Earlier, Elena Rybakina pulled out of her clash against Noskova with a back injury, a day after the Kazakh secured the last qualifying spot for next month's season-ending WTA Finals in Riyadh by reaching the semi-finals in Tokyo.
"I'm very sorry I can't play today," Rybakina said.
"I've been having problems with my back this week and can't play 100%. I'm disappointed that my fans will not see me today but I hope to see you next year."
Noskova, who was beaten in the China Open final earlier this month by American Amanda Anisimova, will aim to capture only her second WTA title having triumphed in Monterrey last year.