The Pole, who is now sixth in the table on 574 points, beat Austria's Stefan Kraft to fly to glory on home snow, triumphing by 5.1 points after a brilliant second jump of 140 metres.
Stoch's two jumps scored an overall 295.7 points, with his second effort proving decisive after just 0.5 points separated him and Kraft at the halfway stage.
Stoch's compatriot Dawid Kubacki claimed the final spot on the podium with a total haul of 287.8 points, while the German duo of Stephan Leyhe and Karl Geiger finished a respective fourth and fifth.
And it is Geiger who still leads the overall standings with a formidable 931 points, closely followed just 48 points behind by Kraft while Japanese jumper Ryoyu Kobayashi is in third.
But Kobayashi endured a difficult time in the Polish mountains, only placing seventh following a disappointing second jump of 134 metres.
The men's ski jumping World Cup heads to Kobayashi's home nation next weekend as the contingent take to the slopes in Sapporo, where the 23-year-old will be vying to replicate Stoch's heroics in triumphing in front of his expectant local crowd.