The Frenchman finished 0.45 seconds clear of Croatia's Filip Zubcic on Monday morning, less than 24 hours after claiming his fourth career Alpine Combined crystal globe.
Pinturault's victory moves him above Aleksander Aamodt Kilde – who finished sixth in Monday's event - in the men's World Cup standings, with 26 points now separating the top two.
The new leader's 14th career World Cup Giant Slalom victory draws him level with Hermann Maier and Benjamin Raich in the all-time list.
Norway's Henrik Kristoffersen was third in the Giant Slalom and also sits third overall, 107 points adrift of top spot.
'Spectacular skiing' - Pinturault triumphs in Hinterstoder