The 32-year-old Pole produced jumps of 141,5 and 135,5 metres to capture his ninth career World Cup victory, and fourth only this season.
Kubacki beat Austria's Manuel Fettner who came second and Slovenia's Anze Lanisek who was ranked third.
Poland's Piotr Żyła came fifth overall on Sunday.
A day earlier Kubacki was ranked second, with his countryman Żyła on the lowest step of the podium. Another Pole, Kamil Stoch finished eighth.
After eight individual events this season, Kubacki tops the overall World Cup standings, with 650 points, ahead of Lanisek with 576 points and Austria's Stefan Kraft with 467.
The 2022/2023 ski-jumping World Cup circuit, run by the International Ski Federation (FIS), features a total of 39 competitions, including 32 individual events, in various countries.
The competition in Engleberg was the last test for the Polish team before the prestigious Four Hills Tournament held in Austria and Germany
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Source: PAP