In front of his home crowd, he finished second in the first round of jumps, with a distance of 139.5m earning him 128.2 points.
In third place at the halfway point was Norwegian Marius Lindvil, half a metre ahead and with 126.1 points.
Geiger rounds out World Cup season with flying finale
Kamil Stoch's 139.5m and 129 points had him in first place after one jump each.
On the second round it appeared that Lindvik would claim the title at Willingen, but neither he now the Polish jumper Stoch could match Leyhe's second-round jump of 144.5m
'Hey ho!' - Wonderful winning jump by Leyhe secures Willingen title
1. Stephan Leyhe (GER) - 266.4 points
2. Marius Lindvik (NOR) - 262.4
3. Kamil Stoch (POL) - 254.6
4. Stefan Kraft (AUT) - 253.5
5. Karl Geiger (GER) - 252
Geiger grabs flying hill gold in tough conditions in Planica
Magnificent Marius toasts first World Cup win of the season in Zakopane