Probably the most versatile skier produced by France since Jean-Claude Killy, Pinturault clocked two minutes 32.42 seconds on the Kandahar course to beat Austrian World Cup leader Marcel Hirscher and triple world champion Ted Ligety of the United States.
It was Pinturault's fourth World Cup victory, all in different disciplines as the 21-year-old from Courchevel has also won a slalom and a super-combined this winter and a parallel slalom last season.
"It's a very important victory because giant slalom is the discipline in which I had my first podiums," said Pinturault, who was twice junior world champion in the speciality.
"I was not far, I was always close but I finally found my way to the top of the podium," added the Frenchman, who straddled the final gate in Val d'Isere in December as he was comfortably leading a giant slalom.
Below par in the morning run and suffering from influenza, slalom world champion Hirscher fought back in the second leg to finish 0.60 seconds adrift.
The Austrian increased his overall World Cup lead, heading Norway's Aksel Lund Svindal, who finished sixth in the German resort, by 209 points.
Perhaps a little tired after his three world golds in Schladming this month, Ligety had to be content with third, 0.63 off the pace.
"It's hard to be disappointed by a podium spot but I frankly didn't come to Garmisch to finish third," Ligety said.
"I might have been a little tired after the worlds but I was also surprised by the soft snow and was never able to deliver one of my usual runs," said the American, who admitted that Pinturault was above the rest on the day.
"It's a great honour to receive such plaudits from the man who has been our inspiration since the start of the season, pushing us to give our very best. I'm extremely flattered," the Frenchman responded.
Garmisch-born Felix Neureuther was fastest in the first leg but cracked under pressure in the afternoon and finished 12th.
While the men's circuit moves to Kvitfjell in Norway next weekend for a downhill and a super-G, Ligety will be travelling to Sochi to train on the 2014 Olympic course.