Compatriot Stefan Kraft had been leading the overall standings heading into the final leg with Tschofenig third.
But the 22-year-old Tschofenig pulled off the biggest success of his career, scoring 1,194.4 points to finish 1.4 ahead of Jan Hoerl with Kraft third at 4.1 for an Austrian podium sweep.
Kraft -- the last Austrian to win the Four Hills in 2015 -- had been leading before the final jump, but recorded 137.5 metres after having waited a long time for regular wind conditions with Tschofenig leaping 140.5 m.
This is only the third time in 73 editions, after 1975 and 2012, that Austria have dominated the Four Hills podium.
"It's incredible, I was really struggling on this hill, but everything fell into place during the second jump. Stefan (Kraft) was the best today and probably deserved to win," admitted Tschofenig.
The pair had two wins each this year with Tschofenig best at Garmisch-Partenkirchen, Germany and Bischofshofen, with Kraft winning at Oberstdorf, Germany and Innsbruck, Austria.
"It's difficult to accept. It's the second time that this has happened to me," said Kraft regretting Monday's event "did not take place in regular conditions".
Since the last Austrian victory a decade ago, Poland and Japan have dominated, with Kamil Stoch and Ryoyu Kobayashi both triumphing three times each.
Japan's Kobayashi, winner of the event in 2024, finished in 15th place.
