Humphries finished in 1 minute, 43.07 seconds for the two runs, beating Martini by 0.42 seconds.
Americans Elana Meyers and Aja Evans finished eighth, while Lolo Jones and Jazmine Fenlator were 10th.
The Koenigssee course is the oldest artificial ice track in the world.
Slovenia surprisingly won a ski jumping World Cup team event in Zakopane, Poland, capitalizing on a late mistake by host Poland and sub-par performances from the usual favorites.
The Polish team led for most of the competition until Krzysztof Mietus had a disappointing second jump in the second-to-last round. The Slovenian team of Yurij Tepes, Robert Kranjec, Yaka Hvala and Peter Prevc took full advantage, finishing with 963.5 points for the victory. Poland was second with 954.4, while favorite Austria came in third with 931.1 points.
Austria still leads the Cup of Nations with 2,850 points, while Germany is second with 2,626 and Norway is third with 2,352.
Five-time champion Sven Kramer took a step toward his sixth European allround speedskating title by winning the 5,000-meter race in Heerenveen, Netherlands.
The reigning Olympic champion and world record holder powered around the Thialf oval in 6 minutes, 12.55 seconds, more than 5 seconds quicker than teammate Jan Blokhuijsen, who was considered the only skater with a chance to upset Kramer.
Sverre Lunde Pedersen of Norway was third.
In the competition's first event, Konrad Niedzwiedzki won the 500-meter race in 35.93 seconds, one-tenth of a second ahead of his Poland teammate Zbigniew Brodka. Havard Bokko of Norway was third.
Kramer leads the allround standings ahead of Blokhuijsen and Bokko with the 1,500 and 10,000 scheduled for Saturday and Sunday.
Austrian snowboarder Andreas Prommegger won a men's parallel slalom night event in Bad Gastein, Austria, for his 10th snowboard World Cup victory.
Prommegger, who is the defending overall champion, edged Roland Fischnaller of Italy by 0.11 seconds in the final.
Zan Kosir of Slovenia beat Justin Reiter of the United States to take third.
Amelie Kober of Germany won the women's event by defeating Marion Kreiner of Austria for her first victory of the season and 12th overall.
Kreiner led the race but lost speed after a mistake shortly before the finish. Claudia Riegler of Austria was third.
It was the first World Cup race under a new single-run format. A parallel slalom with the traditional two runs is scheduled for Saturday.