The Montreal native entered Sunday in fifth place after her first run down the slope, but roared back with a strong second run for the second spot on the podium.
"I was really happy to make a comeback on the second run which was a lot tougher than first one," said Dufresne. "I gave all I had and it paid off."
Nikola Bubakova of the Czech Republic collected her second gold of the competition, clocking a two-run time of one minute 22.95 seconds. Dufresne came in at 1:23.88 while Elvedina Muzaferija of Bosnia-Herzegovina took the bronze in 1:23.91.
Katie Fleckenstein of Whistler, Calgary's Stephanie Profitt and Kristina Natalenko of New Westminster, B.C., were fifth, sixth and seventh.
In the men's giant slalom, Mikkel Solbakken of Norway completed a golden sweep of all three events, clocking 1:50.09. Norway's Lucas Braathen was second in 1:53.21 and Hiroto Hasebe of Japan placed third in 1:53.26.
Montreal's Justin Vittecoq was fourth in 1:53.50.
"I missed all of last season with a broken collarbone so just being at the Whistler Cup this year is a big step for me," said Vittecoq.
Norway placed first in the Nations Cup standings with 235 points, followed by Canada at 153 and Japan at 104.
Dufresne won the Nancy Greene Award as the top Canadian female skier of the competition and Kyle Alexander of North Vancouver, B.C. took the Dave Murray Award as the top Canadian male.