The result means that Kento becomes the first Japanese men's winner in the Badminton World Federation (BMF) Superseries since its inauguration in 2006.
World number 10, Kento beat Hu 21-17, 16-21, 21-15 at the Singapore Indoor Stadium to get the winner's cheque of US$22,500 (S$30,785).
In a chat with media afterwards Kento said things were tense but his determination got him the win in the end.
"There was pressure piling up before today's match, but although I was concerned about it, I was determined to show I was able to win the match," said the 20-year-old.
"Hu Yun plays a very offensive game, so the key was to stay patient throughout the three sets," he added.
The women's final was a close affair with China's Sun Yu saving three match points to beat Tai Tzu-ying of Taiwan for her first Superseries win.
The 21-year-old ended up winning 21-13, 19-21, 22-20.
"I'm overjoyed. I came to Singapore last year and it was the first time I got into the semi-finals but lost eventually, “she said afterwards.
"Now it's my second time and I won the championship, so Singapore must be a lucky place for me," she added.
In the mixed doubles, Chinese top seeds Zhang Nan and Zhao Yunlei were handed a walkover against compatriots Lu Kai and Huang Yaqiong.
The reason for the walkover according to a statement was due to Lu aggravating a knee injury.