Kagiyama missed all of last season after hurting his ankle but he finished third at the French Grand Prix earlier this month and upped his game in front of his home fans in Osaka.
Leading after the short programme, the 20-year-old earned a free skate score of 182.88 points.
He fell on one jump but his overall score of 288.39 was enough to hold off Uno on 286.55 and third-placed Lukas Britschgi of Switzerland on 254.60.
Kagiyama said being last out onto the ice was "nerve-wracking".
"I didn't really think about the outcome until I was finished -- I just focused on the things I needed to do on the ice today," said the Beijing Olympics silver medallist.
"Of course the fall on the axel was disappointing but I was able to stay calm and execute all the elements."
The result meant both Kagiyama and Uno qualified for next month's season-ending Grand Prix Final in Beijing.
Uno also finished runner-up at the Cup of China earlier this month.
"I think my artistic expression and jumps were both very good," said Uno.
"The competition has just finished so there are lots of different emotions but I'm happy with how I performed."
American Ava Marie Ziegler won the women's competition ahead of compatriot Lindsay Thorngren and Belgium's Nina Pinzarrone.
Ziegler was in fifth place after the short programme but a personal-best free skate score of 138.46 gave her the title with an overall 200.50 points.
The 17-year-old said she used her position after the short programme to "motivate" her.
"I know that I could do better and I really used it to push me to be the best that I could be today," she said.
Thorngren led after the short programme but fell to second with an overall score of 198.73.
Pinzarrone, who was third with 194.66, was the only woman to qualify for the Grand Prix Final after finishing second at the French Grand Prix.
Germany's Minerva Fabienne Hase and Nikita Volodin won the pairs title.
Britain's Lilah Fear and Lewis Gibson took the honours in ice dance.
