The 21-year-old from Whistler, B.C., who won gold at last month's Sochi Olympics, lost out to her rival Fanny Smith of Switzerland, but still leads the women's standings with 660 points over Smith and 26-time World Cup winner Ophelie David of France.
"If the overall comes I will be really happy because I've worked really hard this year, but Fanny has too," Thompson said. "I think it will come down to the last race. It was tight out of the start today, and in the final I didn't have my best start."
Swedish teenager Sandra Naeslund won the bronze.
Thompson made history in 2012 when she became the first Canadian to win an individual ski cross Crystal Globe. She's been the picture of consistency this season, winning gold in Sochi plus five World Cup podiums. She's been in the top five in all nine World Cup races.
Georgia Simmerling of West Vancouver, B.C., finished 11th overall after being eliminated in the quarter-final stage. Danie Sundquist of Calgary was also knocked out in the quarter-finals to finish 16th.
Sweden's Victor Oehling Norberg won the men's race.
Backed by a partisan home crowd, Oehling Norberg won every heat and grabbed 1,000 points before Jonathan Midol of France and Swiss Armin Niederer, who got 800 and 600 points, respectively.
Oehling Norberg remains in the overall lead with 521 points, ahead of Swiss Alex Fiva and Andreas Matt from Austria.
It was a disappointing day for Canada's men. Dave Duncan of London, Ont., who was leading the overall standings prior to Saturday's race, went out in the qualification round. Chris Del Bosco of Montreal, Calgary's Brady Leman, Mathieu Leduc of Comox, B.C., and Louis-Pierre Helie of Berthierville, Que., all failed to make the quarter-finals.