The 26-year-old officially handed over the World Cup crown having won it for the past three seasons to Eric Frenzel on Friday with the German winning the first of two events in Norway on Friday.
However it was the Frenchman, a triple gold medallist at the recent World Championships in Val di Fiemme, and not Frenzel who closed the World Cup season with victory in Oslo.
With two jumps and a 15km cross-country ski schedule for the finale, Lamy Chappuis made up a deficit of over a minute to win a three-way sprint finish, which involved Frenzel.
Lamy Chappuis clocked 42:06.5minutes, beating Frenzel by 0.4seconds, with Wilhelm Denifl finishing third in the sprint finish 1.5 behind in total but 3.6 ahead of Akito Watabe in fourth.
Taihei Kato led the way after the two jumps, scoring 246.4 for a margin of 29 seconds ahead of Japanese teammate Yoshito Watabe, who scored 239.2, going into the cross-country ski.
Frenzel placed third with 237.9 for a deficit of 34 seconds while Mario Seidl was fourth, Denifl fifth, Haavard Klemetsen sixth and Akito Watabe seventh before Lamy Chappuis in eighth.
That placed the Frenchman 1:16minutes behind Kato however by the halfway stage of the 15km ski he was part of a seven-strong leading pack that narrowed to five by the 10km mark.
Kato and Akito Watabe fell away as the finishing line beckoned with Lamy Chappuis getting the better of Frenzel and Denifl for just his third win of the World Cup season in Oslo.