Having led the field overnight by 0.23 seconds following the first run in Switzerland on Saturday, Neureuther looked on track to take his second slalom victory of the season heading into the final section.
But a late error which saw him stand on the inside of his ski cost him vital time, and despite recovering, he crossed the line for a total time of 1:34.21 minutes, 0.34 secs behind Pinturault.
For the Frenchman, it proved a sweet victory having three times finished in second spot this season, twice in the giant slalom and once in the super combined while it was his fifth career World Cup win.
Austria's Marcel Hirscher, winner of the slalom event in Adelboden last weekend, finished third to maintain his lead in the overall slalom standings.
While Pinturault sits third in the overall alpine skiing standings, behind Hirshcer and Askel Lund Svindal.