The reigning downhill world champion finished the race ahead of Tina Weirather of Liechtenstein and Nicole Schmidhofer of Austria, who both were only 0.05 seconds behind the Slovenian.
This is the ninth World Cup career win for the 28-year-old Maribor native and the third in the super-G, with her previous best this season in the discipline being 10th place in Lake Louise, Canada.
"I skied relaxed. There were still some mistakes, but it seems it was enough. I was a bit surprised when I arrived in the finish, especially when I saw how close together we are. It's great!," she told reporters.
"Today the split seconds were in my favour, and someone else could be favoured some other time. It's crazy anyhow," Štuhec said, admitting that the "season is long, I'm facing preparations for the January races."
With the World Cup win number nine, Štuhec became the second-best Slovenian skier in this respect, and now trails only the legendary Tina Maze, who holds what are probably an unreachable 26 wins.
It was only the sixth race for Štuhec after she missed the entire 2017/2018 season and the Winter Olympics as she tore a cruciate ligament in her knee which required surgery and months of rehab.
The double win in Val Gardena propelled her to fifth place in the overall standings with 302 points, with Mikaela Shiffrin of the US being in the lead with 689 points. In the super-G standings, the Slovenian is fourth with 144 points.
Štuhec will appear in the World Cup next on 12 and 13 January in Austria's St Anton, with both the downhill and super-G scheduled.