The three-time Olympic champion posted jumps of 131.5m and 139.5m to top the podium, with Slovenian pair Ziga Jelar and Timi Zajc making up second and third.
"My jumps were very good today, I'm very satisfied with today's competition - even if it was not easy in these conditions", Stoch said after the meet.
Watch: Kamil Stoch’s winning jump in Lillehammer
Ryoyu Kobayashi finished fourth, with Peter Prevc fifth. The win represented Stoch’s 36th World Cup win of is career.
The battle for the overall title looks to be a straight fight between Stefan Kraft of Austria and Germany’s Karl Geiger.
Kraft, second to Kobayashi in 2019, leads Geiger by 140 points with two more individual competitions to come.