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 U.S.
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.
"My first victory in a GS... It's just perfect," he told reporters.
Below-par in the morning run, 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 earlier this month, Ligety had to be content with third, 0.63 off the pace.
Garmisch-born Felix Neureuther was fastest in the first leg but cracked under pressure in the afternoon and finished 12th.