The Swiss skier won her fourth World Cup race so far this season in a time of one minute, 22.86 seconds.
Weirather from Liechtenstein was 3-100ths of a second behind. It is also her fourth time on the podium this season, but she's yet to win, with three silver medals and one bronze.
Anna Fenninger was third, 3-10ths back of the winner. The Austrian hit the podium for the third time this season.
Lindsey Vonn again showed improvement in her return from a knee injury. The U.S. ski star was fifth, after finishing 40th and then 11th in the weekend's two downhills.
"I felt really good," Vonn told CBC Sports after the race. "I'm just making progress every day. Nothing happens overnight, but I think I've made some great progress this weekend."
Vonn tore ligaments at the world championships in February and last month aggravated that same right knee injury with a partial tear of the ligaments.
"The end goal is definitely Sochi and the Olympics," the 29-year-old said.
Vonn added: "I tried to build my confidence and push myself every day [this weekend]."
Canadian Marie-Michele Gagnon of Lac-Etchemin, Que., was 10th, her best ever finish in a World Cup super-G.
Larisa Yurkiw of Owen Sound, Ont., did not finish the course.
Gut's victory denied Maria Hoefl-Riesch of a Lake Louise hat trick after winning the two downhills. Hoefl-Riesch was 19th.
Vonn had won all three races in each of the previous two years at Lake Louise.
Last year's dominant World Cup champion, Tina Maze of Slovenia, was 13th on Sunday.
Gut now leads the World Cup overall standings with 446 points, followed by Hoefl-Riesch (405) and Fenninger (345). Canada's Gagnon is 13th.
The women's tour heads to St. Moritz, Switzerland for a super-G and giant slalom next weekend.