Last week saw the Japanese skater take his place on the podium for the first time, coming third in the 500m, but this time around there was no stopping him on the ice.
The 22-year-old beat Pavel Kulizhnikov in the third last pairing, with his time of 35.45 seconds proving the fastest of the day in Tomakomai.
Compatriot Yuma Murakami bagged silver in 35.53s, while world champion Dutchman Jan Smeekens rounded off the podium five hundredths of a second further back.
Kulizhnikov's time of 35.80 was only enough for sixth place but the Russian still holds the World Cup lead with 138 points.
Olympic champion Havard Lorentzen had to settle for 11th in this 500m outing, sitting in third in the World Cup standings behind Shinhama.
Meanwhile a late change proved vital for the Netherlands en route to victory in the team pursuit.
Once again they met last week's victors Russia in the final but this time they replaced Chris Huizinga with world all-round champion Patrick Roest.
Roest therefore acted as a more-than-able engine with Marcel Bosker and Douwe de Vries also laying down a marker as the Netherlands stopped the clock in 3:45.87.
Russia had to settle for fourth place with silver and bronze going to Norway and Japan respectively.