The Austrian soared to an imperious total points tally of 268.5 on the Japanese slopes, holding off Geiger's German compatriot Stephan Leyhe by 21.1 to now sit 63 points clear at the top of the table.
Home favourite Ryoyu Kobayashi finished third, while Slovakia's Peter Prevc came fourth and Geiger languished down in fifth in what represented a blow to his World Cup chances.
Kraft got the ball rolling with a formidable first jump of 139 metres to open up a commanding early lead, before executing a carbon copy of that height in his second to render Leyhe's effort of 142 metres in vain.
Kobayashi, Geiger and Poland's David Kubacki had all started promisingly with impressive first jumps, but disappointing second attempts saw them all leapfrogged by the resurgent Leyhe.
Leyhe's second-place now leaves him eighth in the World Cup standings on 510 points, while Kubacki is third on 924 â€“ 139 behind Kraft â€“ and Kobayashi lies fourth on 907.
The ski jumping World Cup heads to Willingen, Germany, next, where Geiger has the opportunity to cut the deficit to Kraft at the top of the table in front of an expectant home crowd.