A winner of three previous individual World Cup events, Freitag entered Saturday's competition having finished no higher than 10th in five outings this season.
However, an impressive second jump saw the 23-year-old German edge out Roman Koudelka on this occasion, with Michael Hayboeck and Jernej Damjan sharing third.
Freitag, whose last success had come at Lahti in March 2013, sat fourth after the first round of jumps, behind Hayboeck, Peter Prevc and Koudelka.
However, a second jump of 135.5 metres saw Freitag overhaul his rivals to finish with 277.7 points, 0.6 ahead of Koudelka.
Hayboeck and Damjan were a further 0.9 points back, while Prevc took fifth with 274.8 points.
World Cup leader Anders Fannemel finished well down the field in 21st, enabling Severin Freund, who finished seventh, to close within 43 points of his rival at the top of the standings.
Hayboeck now sits third, with Koudelka fourth and Prevc, last year's World Cup runner-up, in fifth.