The German, whose other triumph this campaign came at Engelberg in December, secured success with 278.5 points from his two jumps on the hill in Austria.
Freitag recorded a jump of 133.5 metres on his first attempt, before making sure of the win with a second effort of 132m.
The 23-year-old's performance was enough to edge out home hope Stefan Kraft (273.5) by five points, with four-time Swiss Olympic gold medallist Simon Ammann and Noriaki Kasai (both 263.7) sharing third place.
Michael Hayboeck (257.5) was only good enough for sixth place despite setting a new hill record of 138m with his final jump, beating the 137m mark Kraft had set with his first attempt.
Kraft stands atop the Four Hills standings with 835.4 points. Hayboeck is his closest challenger with 812.3 and the pair will fight it out to become the seventh consecutive Austrian winner of the Four Hills in the final round at Bischofshofen on Tuesday.
Hayboeck leads the overall World Cup standings with 589 points, 32 ahead of second-placed Kraft.