The Pole had not tasted victory since mid December when he topped the medal rostrum on two consecutive weekends in Titisee-Neustadt, Germany and Engelberg, Switzerland.
But he began a new month by taking the win in the night event in Germany in what is the last meeting before the Winter Olympics begins next week.
Jumps of 139.5m and 145.5m handed him an overall score of 263.2 points, narrowly edging out home favourite Severin Freund by a single point.
While Slovenia's Jernej Damjan continued his recent run of podium finishes in third to build on his gold and silver in recent weeks.
It leaves Stoch second in the overall World Cup standings on 821 points, 27 behind leader Peter Prevc who defended his yellow bib by finishing fifth.