Ammann, who finished seventh overall last season, produced a consistent showing on the 142-metre hill, taking victory by eight points from Daiki Ito.
Even though he did not have the longest jumps of the competition, the 33-year-old scored highly on the judges' points on a foggy evening in Ruka to finish with a combined total of 284.1.
Ammann and Ito were well clear of their rivals after the first round of jumps, both men scoring over 140 points, with Severin Freund was their nearest challenger on 136.7.
And it was the Swiss who held his nerve on the second attempt - the last of the competition - with a 142-metre leap earning 143 points and confirming his victory in style.
Austria's Andreas Kofler produced the longest jump of the day as he flew 144.5 metres in the first round, but he failed to impress the judges with his style and subsequently lost points.
Kofler had to settle for fourth place, though, as Noriaki Kasai recorded a final-round jump of 136.2 points, nudging him onto the podium.
In doing so, the 42-year-old broke his own record for the oldest individual World Cup podium, and with Ito became the first pair of Japanese jumpers on the same podium since 2006.