The Czech seventh seed clinched her second WTA Tour title of the year - following her February triumph in Dubai - but had to do it the hard way after the world number nine from Germany pulled off a bagel set to force a tense decider.
Kvitova had fired 17 winners to just five unforced errors in the first set but watched former US Open semi-finalist Kerber speed through the next six games to keep her hopes of a third career victory alive in the Japanese capital.
But the 2011 Wimbledon champion rallied convincingly, storming to a 4-0 lead before closing the match out inside an hour and 39 minutes with a huge crosscourt forehand on the 19th shot of a rally to earn her 11th career title.
She told wtatennis.com: "In the first set I was attacking every ball and hitting so many winners but in the beginning of the second set I made some easy mistakes and felt slower in my legs, and that's what Angie was waiting for.
"I knew it wasn't over until the last point, though. After the second set I knew what I had to do - play the same way as the first set, stay aggressive and cut the mistakes down again.
"I'm very happy I could win this final today. For me the whole tournament was great - I felt good all week on the court. I really enjoyed my week here and it's even better to come away with the title."
The final was also a first between left-handed players on the WTA Tour since Melinda Czink beat Lucie Safarova for the Quebec City title in 2009.
Kvitova and Kerber next head to Beijing for the China Open, with the Czech saying: "I'll take a day off from tennis maybe.
"Then I'll think about my first match there."