The 26-year-old had seen the gap in the overall standings close a day earlier after nearest rival Geiger triumphed in the first event of the weekend's double-header in Romania.
But Kraft improved on his Friday performance, which saw him finish third, as jumps of 103m and 97.5m saw him post a total of 270.3 points to get the better of Geiger.
Geiger's jumps of 99.5m and 96m were enough for him to claim second place ahead of compatriot Schmid, who celebrated his first World Cup podium with jumps of 103m and 95.5m.
Poland's Dawid Kubacki just missed out on the top three as his points total of 258.6 after jumps of 96m and 100m meant he finished behind Schmid (260.2) and Geiger (266.7).
But Kubacki's fourth-place finish did help him move up into third in the overall World Cup standings, ahead of the absent Ryoyu Kobayashi, with Kraft leading Geiger by 118 points.