The Frenchman produced a masterful run of 38.92 seconds in the slalom, as he set a total time of 1:47.71 to top the podium in Sweden.
Watch Pinturault's winning run at the World Championships
He was only 24th after the downhill but his run in the second discipline, the second fastest of all skiers, was enough for victory.
Slovenia's Stefan Hadalin had to settle for the silver medal as he finished 0.24 seconds short of the winner despite producing the fastest time on the second run.
Austria's Marco Schwarz was a further 0.22 seconds behind as he completed the top three.
Dominik Paris, from Italy, was fastest in the downhill as he crossed the line in 1:07.27, but he could not hold onto the lead and finished in ninth place overall.
Paris loses big time on slalom run to miss out on podium finish