The Swiss, who won the bronze medal in the downhill at the 2014 Sochi Olympics, clocked a time of one minute, 02.68 seconds, finishing 0.10 seconds ahead of Tina Weirather of Liechtenstein. Italy's Sofia Goggia was third in 1:03.27.
Overnight snow flurries and poor visibility delayed the start of the race 75 minutes so organizers could make sure the track was safe to ski on.
Gut had to plough through some thick snow for her win but it turned out to be the perfect storm for the 25-year-old from Lugano, Switzerland.
She not only took advantage of the organizers' decision to shorten the super-G course because of the bad weather, but the flat terrain -- that makes Lake Louise one of the less demanding speed courses on the circuit -- suited her game plan.
"I am finally leaving Lake Louise with a full smile," Gut wrote on her Twitter account. "And the slope didn't get any steeper, hehehe."
Gut showed steady improvement as the first speed races of the 2016-17 FIS Ski World Cup season kicked off in the Canadian Rocky Mountains with a pair of downhills followed by the super-G.
In the back-to-back downhills she finished fourth on Friday and second on Saturday behind Ilka Stuhec.
"Yesterday and the last days, I had the feeling I was finally starting to build something," Gut said.
"I wasn't skiing really well at the top. So I understood that I should change something, and from the middle on I tried to keep a really straight line and be aggressive. I'm happy it paid off."
I'm finally leaving from Lake Louise with a full smile! :) and the slope didn't get any steeper, hehehe https://t.co/gcMr1Zr7e1— Lara Gut (@Laragut) December 4, 2016
Weirather skied from the fifth starting position and set the early pace.
She said her first podium finish of the young season has given her a confidence boost.
"I was pretty angry after yesterday, so I tried to put that anger into skiing today," she said of her ninth place finish in Saturday's downhill.
"That helped me for sure and now the confidence is up and I hope to keep it going."
Slovenia's Stuhec, who also won Friday's downhill race, finished fifth in the super-G with a time of 1:03.42.
Sweden's Kajsa Kling was fourth with a time of 1:03.38. Kling placed a surprise third in Friday's downhill.
The ladies now head to Sestriere, Italy, for a giant slalom on Saturday.