Kueng took victory by 0.24seconds in 1:21.73minutes for Switzerland's first podium finish in a men's speed event since March 2012 and his first-ever win in any discipline at the World Cup.
His only previous podiums were one second and one third place finish, both in downhill, while Otmar Striedinger was second and Hannes Reichelt and Peter Fill joint third.
Kueng's win ended Aksel Lund Svindal's bid for a fifth straight super-G win under his belt, which would have been a record for most consecutive in the discipline, and he was as surprised as anyone.
"It's a really strong group of guys competing right now and it is not so easy to get on the podium so I am especially happy with the result," said Kueng.
"I had a good line at the bottom and was able to keep my momentum through the flatter part. That helped me a lot."
Elsewhere in Lake Louise, double Olympic champion from Vancouver 2010 Maria Hoefl-Riesch claimed victory yet again in the second of two downhill events; repeating the feat of 24 hours ago.
She clocked a winning time of 1:55.09minutes with Tina Weirather second in 1:55.43 and Anna Fenninger third in 1:55.56; Lindsey Vonn an impressive ninth as she comes back from injury.