The victory means Prevc now heads the tour, which goes into its last two events in Austria.
Prevc led Severin Freund of Germany after the first heat with a jump of 133.5 meters.
He then made the longest jump of the day and finished with a victorious total of 272.7 points.
Freund, who won the opening leg in Oberstdorf last week, is now on third place behind Kenneth Gangnes of Norway, who came in second with 134 meters.
Gangnes jumped 132m in the first heat for a total of 260.1 points.
In the Four Hills standings, Prevc leads on 572.6 points, Freund with 564 and Hayböck at 551.5.
The tour continues on Sunday in Innsbruck.