The 24-year-old led from start to finish over the short distance to claim her third successive title in the event in the 2019-20 season.
Boutin stormed to victory in 43.374 seconds with Italy’s Arianna Fontana claiming silver and Korea’s Kim Ji Yoo completing the podium.
"That was perfect. I tried to be smooth and really control the race and I think it worked for me," Boutin said.
"It’s really nice because we work on it and it’s really great when you practise and then succeed on the ice in competition, so I’m really proud of that.
"It’s been good work at training [that’s helped with the results] and my goal is to keep this focus, to keep strength and to be comfortable – and uncomfortable – to be better."
Boutin went home with another medal from Nagoya as Canada secured silver in the Ladies 3000m relay where they beaten to top spot by Italy and Russia finished third.
Suzanne Schulting, from the Netherlands, bounced back from defeat in the 1000m final to clinch victory in the Ladies 1500m  after taking the lead with two laps remaining.
In the men’s 1500m , Korea’s Park Ji Woo won his second gold of the weekend as he beat compatriot Lee June Seo to first place while Japan’s Ibuki Hayashi came third.
Hungary’s Shaoang Liu produced a dominant performance in the men’s 500m final to take victory ahead of Russia’s Pavel Sitnikov and Korea’s Park In Wook.
While China won the final medal race of the weekend as they secured top spot in the Men’s 5000m Relay ahead of Korea and Russia.