The Calgary native finished with 1,629 points, one more than Meyers. If Humphries — the Olympic champion and now a two-time overall World Cup winner — was 0.03 seconds slower Sunday, Meyers would have won the title.
Humphries and Heather Moyse of Summerside, P.E.I., finished with three World Cup victories, one silver and one bronze medal.
One of the most explosive teams out of the start, the pair set a new women's start record in Konigssee at 5.17 in both runs.
"Kaillie crushed everyone in that first run and I thought she was going to cruise to a win today," said head coach Tom De La Hunty. "But she made a mistake on that second run and when you make a mistake in a snowy race it pays you back double."
Fabienne Meyer and Tanja Mayer of Switzerland won the last race of the season in a two-run time of one minute 44.01 seconds. Meyers and Aja Evans had a stellar second run to climb six spots and finish second, just ahead of Humphries and Moyse.
Jennifer Ciochetti of Edmonton, and Chelsea Valois of Zenon Park, Sask., were 12th at 1:45.31.
Canada also won bronze in the four-man race. Lyndon Rush of Humboldt, Sask., Lascelles Brown of Calgary and Edmonton's David Bissett and Neville Wright finished two runs in 1:38.84.
The defending Olympic four-man champion Steven Holcomb and his team won their fourth race of the year in 1:38.54, edging the Swiss sled driven by Beat Hefti by a mere 0.09 seconds.
Holcomb medalled five times in eight four-man races this season, finishing second to Germany's Maximilian Arndt for the yearlong points title. Holcomb was the two-man season champion.
Feeeding off his first World Cup two-man victory, Justin Kripps and his crew finished 11th in the four-man. Kripps of Summerland, B.C., James McNaughton of Newmarket, Ont., Tim Randall of Burlington, Ont., and Edmonton's Bryan Barnett stopped the clock at 1:39.25.
Calgary's Chris Spring finished fifth in the overall World Cup four-man standings with a 12th place finish on Sunday. Spring and his crew of Jesse Lumsden of Burlington, Ottawa's Cody Sorensen and Saskatoon's Ben Coakwell posted a time of 1:39.31.