Second behind the Austrian after the first leg, the German handled the tough conditions of the floodlit second run better to beat Hirscher by 0.36 seconds with Italy's Manfred Moelgg in third.
The 29-year-old Neureuther, who finished second four times behind Hirscher last season, proved with his sixth World Cup victory that he was a major threat at the Olympics despite an injury-plagued season.
But the German, who skied with a bandaged wrist after a spectacular crash in Levi in November, repeated comments made to German magazine Der Spiegel expressing concern about the situation in Russia.
"I said that I was concerned about the human rights situation in Russia, that everything was not right and that the IOC should check how and where they award the Games," he told reporters, hinting at the controversial anti-gay laws recently voted in in Russia.
"It is not right that the Games should go to the places with the most money. The priority should go to sport and to the emotion spectators feel when they attend the Olympic games," added Neureuther, the son of double Olympic champion Rosi Mittermaier.
"To have the Olympics in Sochi or Pyeongchang or the soccer World Cup in Qatar is not good for sport. They should definitely go in other directions in the future," added the German.
Asked if he was planning a protest to express his views in Sochi, he said: "I'll pretend that I'm gay. No, it's a joke. I will concentrate on sport, that's the most important thing."
- Sports & Recreation
- Manfred Moelgg