Lamy Chappuis, fifth after the jumping session, started 46 seconds behind the leader but whittled down the gap and pipped American Johnny Spillane by less than half a second at the finish of the 10km cross country race.
Spillane's silver was the first US Olympic medal in the Nordic Combined event.
Italian Alessandro Pittin came third, just beating veteran American Todd Lodwick for the bronze.
Lamy Chappuis, who has a commanding lead in this year's World Cup standings, sat just behind Spillane for much of the last lap before making his move.
"In the last stretch I told myself I had to seize my chance. I've improved my skiing a lot this season and that allowed me to give it my all in the final sprint," he said.
Vincent Jay earlier won France's first gold in the 10km biathlon sprint.
The result was also a personal triumph for Spillane, who has had a series of injury problems since winning an individual world championship title in 2003.
Various medical mishaps wrecked five seasons of competition and last year he had two rounds of knee surgery, which prevented him from training between July and November.
"I was wasting so much energy on recovering from injuries that instead of trying to get better at Nordic Combined I was just trying to get healthy," he said.
"(It’s) a little bit more fun when you’re having good results and not just feeling hurt all the time."
US head coach Dave Jarrett said he was inspired by the performances of Americans Todd Lodwick, who came fourth, and by Bill Demong, who made up more than a minute to finish sixth.
"We’re fired up to move on. I know Todd and Bill are, I guess, jealous of Johnny now and they want to be there with him," he said.
Finland's Janne Ryynaenen started the cross country with a 34-second advantage after winning the jump but fell early on and was quickly overtaken.
Strong contenders like Austrian Felix Gottwald and Norwegian Magnus Moan never recovered from poor jumps caused by rapidly shifting weather conditions and started at the back of the field.
Place of birth: Missoula, Montana, United States
Residence: Bois D’amont, France
Previous Olympic results:
Fourth place, 2006 Winter Olympics, individual lh 7.5km CC
Fifth place, 2006 Winter Olympics, Team lh 4x5km CC
11th place, 2006 Winter Olympics, individual nh 15km CC
Bronze medallist, 2009 world championships, individual lh/10km cc
Bronze medallist, 2009 world championships, mass start 10km cc/nh
Champion, 2006-07 World Cup, individual
Runner-up, 2007-08 World Cup, individual sprint Runner-up, 2006-07 World Cup, individual
Lamy Chappuis, who leads this season’s World Cup, started skiing at two years old and developed a passion for ski-jumping in 1995. He is a qualified pilot and works as a customs officer.
His Vancouver victory came in dramatic fashion. After starting the cross country 46 seconds behind the leader, he whittled down the gap to pip American Johnny Spillane at the finish line.