Guay won narrowly with a time of 1 minute, 56.65 seconds, just 0.12 seconds ahead of Kjeitel Jansrud of Norway.
"Knowing that I have had knee surgery only this August makes today amazing," said Guay. "I had no training until November but Val Gardena has been good to me, I was third here last year and I knew I could do well again."
The victory moved Guay into eighth place in the overall World Cup standings. Norwegian Aksel Lund Svindal held on to first place after finishing fourth Saturday.
Johan Clarey of France filled out the podium with a third-place run of 1:56.89. Bode Miller of the United States came in fifth with a time of 1:57.04.
Interpol investigating stolen passports on missing flight
Teacher apologizes for showing sexual image of herself in class