Humphries and Lotholz were third following their first trip over the 1,500-metre Sochi track that features three tricky uphill sections. But the Canadians managed to move up a spot following their second run with a combined time of one minute 56.09.
"I made a few mistakes on that first run which cost us time, but that second run was good," said Humphries, who was making her first return to Sochi since winning her second-straight Olympic gold medal nearly one year ago.
The silver completes a medal collection for Humphries in her three trips to Sochi. In addition to her Olympic gold, the 29-year-old Calgarian also won the bronze medal at the Olympic test event in 2013. It was the first trip to Sochi for rookie brakeman Lotholz, 22, also of Calgary.
"I was very proud of Melissa with our starts today," said Humphries. "To come here and finish amongst these (Amercian) women is awesome.
"It is a Happy Valentine's Day."
With their best finish of the season, the Canadians finished second overall on the World Cup with three bronze and a silver in the eight-race season.
American Elana Meyers-Taylor locked up the overall title with her sixth victory of the season. Finishing second to Humphries and her Olympic brakeman, Heather Moyse, last year at the Sochi Games, the American got some redemption Saturday. Meyers-Taylor and Cherrelle Garrett cruised to the gold medal with a time of 1:55.48.
Compatriots Jamie Greubel Poser and Lauren Gibbs were third in 1:56.10.
In the men's event, Justin Kripps of Summerland, B.C. and Edmonton's Bryan Barnett finished fourth with a combined time of 1:53.06.
"We drew No. 1 for the start order and managed to capitalize on the good ice," said Kripps. "We had our best two start ranks of the year and two solid drives.
"This track is really technical and it's quite different from any other track in the world. It is an amazing facility so I always get excited and it is a real pleasure to slide here."
The Canadians finished eighth in the overall standings.
Switzerland's Peter Rico and Simon Friedli won the race in 1:52.33. Latvia's Oskars Melbardis and Daumants Dreiskens were second in 1:52.46, while Beat Hefti and Alex Baumann, also of Switzerland, finished third in 1:52.60.
The Latvians claimed the overall title with 1,684 points, 48 ahead of Hefti and Baumann.
Calgary's Chris Spring and Derek Plug were 14th in 1:54.54 while World Cup rookies, Nick Poloniato of Hamilton and Calgary's Josh Kirkpatrick, finished 16th at 1:55.52.