German Richard Freitag, who was Stoch's main competitor for the title, ended his campaign early after a bad landing in the first round left him injured and unable to compete in the second round.
Stoch, 30, battled heavy rain and strong winds to finish with a total tally of 270.1 points after leaping distances of 130 and 128.5 metres across the two rounds.
Norway's Daniel Andre Tande was second after jumping 129.5 metres in his first attempt and 125 in his second to finish on 255.6 points.
German Andreas Wellinger rounded out the podium after leaping 133 and 126 metres to notch 253.5 points.
Stoch, a gold medallist at the 2014 Sochi Olympics, won the Four Hills tournament last year after finishing second in the first two events and winning the final leg.
Freitag holds an 88-point lead atop the overall World Cup leaderboard while Stoch is second on 623 points ahead of the final Four Hills event at Bischofshofen on Jan. 6.
(Reporting by Aditi Prakash in Bengaluru, editing by Pritha Sarkar)
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