The Frenchman finished in second in a shortened super-G to put himself in pole position for victory in Upper Austria before wrapping up the top prize in the concluding slalom.
Switzerland's Mauro Caviezel finished second on the day after leading the way following the morning's super-G with his time of 1:09.62 edging out Pinturault (1:09.85).
But Pinturault's slalom run of 55.05 was enough to secure the win by 0.99seconds over Caviezel, with Norway's Aleksander Aamodt Kilde completing the podium.
Kjetil Jansrud, also of Norway, was fourth while Austrian favourite Vincent Kriechmayr, who won a regular super-G on Saturday, finished 3.23 seconds behind outside the top 10.
In the overall Alpine Combined title race, Pinturault's victory in two of three combined races saw him finish on 280 points to take the crown ahead of Kilde (172 points).
Pinturault is also one of three remaining contenders for the overall title, with his win in Hinterstoder closing the gap to leader Kilde to 34 points with Henrik Kristoffersen 101 points back in third.
Pinturault takes combined victory and crystal globe