The Japanese scored 245.5 points from his two jumps, ahead of Norway's Anders Bardal in second place with 239.2 points. Czech Lukas Hlava was third with 237.2 points.
The competition was held on a normal hill because of strong winds.
With his second-place finish, Bardal scored 80 points to remain in the overall World Cup lead. The Norwegian now has 1,219 points, 84 ahead of second-placed Gregor Schlierenzauer of Austria. Andreas Kofler of Austria is third overall, 153 points behind Bardal.
Bardal managed the longest jump of the day -- 96 metres -- on his second attempt.