The Dutch skater crossed the line in 1:09.20 to finish in first place and claim his first-ever maximum haul of 100 points to propel him up to fourth in the overall standings after just two rounds.
Canadian Denny Morrison is still sitting pretty atop the overall standings on 225 points after coming second in Japan, with Netherlands' Kjeld Nuis 35 points behind after crossing the finish line in third.
In the other men's race on Sunday home favourite Keiichiro Nagashima claimed victory over 500m, 0.02 seconds ahead of Canada's Gilmore Junio with Dutch skater Jan Smeekens in third in a close race.
Despite finishing third Smeekens stretched his World Cup lead to 30 points over Japan's Tae-Bum Mo from South Korea, who could only finish fifth in Nagano.
In the women's 1000m Canadanian Christine Nesbitt just came out on top in a battle with Heather Richardson, beating the American to the finish line by just 0.13 seconds.
Despite coming second best Richardson also stretched her lead in the World Cup standings to 70 points with her nearest challenger, Lotte van Beek from Holland, could only manage third.
And in the women's 500m South Korean Sang-Hwa Lee took the win ahead of Germany's Jenny Wolf and Japan's Nao Kodaira who finished second and third respectively.
Lee has won all of her events and has already build up a commanding 125 point lead atop the overall standings.