Axelsen, who had only won one of his prior 15 career meetings against his Japanese opponent, dropped a close-fought first game 20–22 despite having been 14–7 ahead at one stage.
However, the Dane levelled the final with a 21–18 second game before running away to a 21–12 third game in which Momota never looked like challenging.
Earlier, there were three Japanese victories – in the women's singles, men's doubles, and mixed doubles finals.
The Korean had taken the first 21–18 before Yamaguchi won a titanic second game 25–23, but the Japanese ran out to a comfortably 16–5 lead in the third before An called it quits.
Hoki Takuro and Kobayashi Yugo stunned the home fans in the men's doubles final as the unseeded pair defeated Denmark's Kim Astrup and Anders Skaarup Rasmussen, the eighth seeds, 21–18 21–12 in straight games.