Sitting in third spot heading into the final run, it appeared the Canadians would drop off the podium for the first time this year.
But a costly error by Germany’s Cathleen Martini stretched Humphries' medal streak to 13.
Germany’s Sandra Kiriasis and Franziska Bertels won gold with a time of 1:57.19.
Americans Elana Meyers and Aja Evans finished second at 1:57.32.
The Canadians finished in 1:57.33 on the same course that will be used at next year's Sochi Olympics.
"They weren’t the best runs today," said Calgary's Humphries. "I made a few mistakes, but I am still learning. We are going to come back here again next year for international training week and work hard to clean things up."
Edmonton's Jenny Ciochetti drove to her personal best result with a sixth-place finish.
It has been an unprecedented medal-winning string for the 25-year-old Humphries that includes two world titles and nine World Cup victories dating back to last season. Humphries set a record when she won eight straight races earlier this year.
"I am super happy with the season overall," she said.
The Olympic champion from Calgary teamed up with Valois, from Zenon Park, Sask., this fall. The duo captured six golds along with one silver and two bronzes and a world title.
"I didn’t know what to expect when I came out to that testing camp," said Valois. "I didn’t know anything about the sport and I just tried to learn as I go. It slowly progressed. I kept working hard and with great people around me I am feeling really comfortable now."
Earlier in the day John Fairbairn led the Canadians in the men’s skeleton race. Focused on making his Olympic debut in Sochi next year, the Calgarian finished ninth in 1:56.13.
"After a number of frustrating races at the end of the season, I feel the pieces came together for me better today and that is a good note to end the season on to bring confidence going into next season," said Fairbairn.
Eric Neilson of Kelowna, B.C., slid into 10th spot at 1:56.23, while Olympic champion Jon Montgomery of Russell, Man., placed 12th.