Flisar was dominant throughout the qualifiers to reach the final, before beating Canada's Christopher Delbosco for the win in the final.
Austria's Christoph Wahrstoetter came in third, while France's Bastien Midol rounded out the finalists.
Midol's compatriot Jean-Frederic Chapuis leads the World Cup standings but went out in the last 32, while Flisar's victory sends him up to fourth overall.
Sanna Luedi crashes out in Ski Cross
Delbosco now lies third, just behind fellow Canadian Brady Leman who went out in the round of 64.
Mahler wins dramatic final for maiden victory
Sandra Naeslund pips Courtney Hoffos in photo finish