The Austrian athlete produced jumps of 135m and 128.5m to register the 15th World Cup victory of his career.
Kraft steals top spot in Sapporo despite Stoch’s new record
He said: "It was an amazing weekend for me. I love Japan now. My jumps today were even better than yesterday.
It's going really well, I'm enjoying it, the hill suits me and, of course, you also need the necessary luck here. I'm extremely happy and proud that I could win three times in a row.
Kraft scored 248.2 points as he finished 9.8 points clear of second-placed Timi Zajc, of Slovenia.
World Cup standings leader and home favourite Ryoyu Kobayashi had to settle for third with a score of 236.6.
The Japanese jumper is still way ahead on 1,233 total points, with Kraft (781) in second and three-time Olympic gold medallist Kamil Stoch in third (744), after a sixth-placed finish in Sapporo.
Geiger rounds out World Cup season with flying finale