The Pole, who claimed the Four Hills title earlier this month, enjoyed more success in Germany as he edged out Ryoyu Kobayashi to clinch the win.
Kubacki led after the first jump with a 3.3-point advantage over his Japanese rival, and while Kobayashi pushed him all the way in the second jump, Kubacki held on by just 0.3 points.
Those two were well clear of the rest of the field, as Slovenia's Timi Zajc took third, 11.7 points behind Kubacki.
Karl Geiger had to settle for fifth place but remains top of the World Cup standings with 886 points, 83 points clear of Stefan Kraft.
Kobayashi sits in third, with Kubacki fourth as the action heads to his homeland in Zakopane.
Lincoln Grand Prix
Stages 19 & 21