Stoch, who claimed the overall crown last year, won with a total of 279.7 points to Freitag’s 275.5.
There was a second Pole on the podium as Dawid Kubacki came in third with 270.1.
Geiger rounds out World Cup season with flying finale
Stoch was someway off the distance after his first jump of 126m, with Austria’s Stefan Kraft jumping 132m.
But Stoch came up with a supreme second jump of 137m amid worsening conditions in the German Alps.
The Four Hills continues on January 1 in Garmisch-Partenkirchen, Germany, before moving onto Austria in Innsbruck (January 4) and Bischofshofen (January 6).
Stoch will be defending two Olympic titles in PyeongChang in February after winning the normal hill and large hill competitions in Sochi four years ago.
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