The Japanese jumper finished over 10 points clear of the field led by Stefan Kraft of Austria, who finished second for the seventh time this season.
Poland's Dawid Kubacki finished in third a further 4.6 points back.
Sato's countryman Ryoyu Kobayashi led after the first round and had the opportunity to win his fourth competition of the season with his last jump but, in difficult windy conditions, he could only manage a 110m jump which saw him slip all the way to 15th.
How Sato turned it around at home
Sato was sixth after the first round but his 138.5 metre jump in the second helped him claim victory, a distance bettered by no one in the competition.
His points total for the round was also the most amassed with a single jump.
The win means Sato becomes the first Japanese ski jumper to take a men's individual World Cup event in Japan since 2012.