The four-time world champion finished off the pace in fifth in the season opener in Kuusamo last month but bounced back in Norway crossing the cross-country finish line 13.5 seconds ahead.
The Frenchman set himself up from the start, finishing second in the ski jumping with a score of 120.6 points behind compatriot Francois Braud who scored 122.6 points.
Braud would eventually finish down in sixth but it was Lamy Chappuis who maintained the pace on the skis, holding off Japan's Akito Watabe followed by Mikko Kokslien of Norway in third.
Germany's Eric Frenzel, winner of the opening individual World Cup event, finished in tenth leaving him third in the season's overall standings.
But it is Lamy Chappuis who now leads the way, 15 points ahead of Norway's Joergen Graabak in second.
"I started with a really good jump, it's always easier to start in front and to give your own pace," said Lamy Chappuis.
"We had a good pace with my team-mate Francois Braud, it was really nice to be together at the front of the race.
"I was a little bit afraid of the Norwegians at the end but I stayed in front which was great. Akito started really fast too."