The 32-year-old could only manage a fourth-place finish in the first event of the season in Carezza as Andreas Prommegger took the win.
But Fischanller blew that out of the water second time around as he beat home favourite Zan Kosir to pick up maximum points.
The win propels Fischnaller to the top of the leaderboard after just two events and is 100 points ahead of Prommegger who finished sixth in Slovakia.
In the women's event it was Russian Ekaterina Tudegesheva who was celebrating a first win of the season as she got the better of Holland’s Nicolien Sauerbreij in the big final.
However unlike Fischnaller the victory was not enough to take her to the summit of the World Cup standings as Canadian Caroline Calve holds on to top spot despite finishing fourth in Rogla.