"It was pretty nerve-racking but I felt good," Kizzire said in a greenside interview after carding 67 to finish at 19-under-par 265.
Fowler, in his first start of the 2017-18 season, birdied the 16th and 17th holes to put pressure on Kizzire but left a long birdie putt at the last short.
He also shot 67 and had to settle for his 12th second-placing on tour to go along with four victories.
The $766,800 consolation prize lifted Fowler over $30 million in career earnings.
It took Kizzire 63 starts to finish on top, but he channelled past experiences that included two wins on the secondary Web.com Tour.
"I've been in tough spots before and I drew from all my experiences," he said. "It means a lot. I'm pretty excited right now, pretty emotional and I was glad to get it done. Rickie made me work hard."
The 31-year-old hopes his win provides the springboard for further success.
"I want to win golf tournaments and it feels good to get it done today. That gives me a lot of confidence. I understand There's a lot of good players out here.
"I just want to keep working hard and win bigger and bigger and better things. The tournament this week was awesome and I was glad to get my first win here."
(Reporting by Andrew Both in Tokyo; Editing by Ian Ransom)
