Fenninger trailed Lindell-Vikarby by 0.02 seconds after the first run at Lienz and then posted another solid time in the second run to come away with a combined winning time of 2 minutes, 17.00 seconds.
The win left Fenninger in second place in the overall women's point standings behind Tina Weirather of Lichtenstein, who finished in a disappointing 17th place.
Mikaela Shiffrin of the United States came in third with a 2:17.51, 0.01 ticks behind Lindell-Vikarby, in the final qualifier for the Winter Olympics giant slalom. She edged fourth-place Kathrin Zettel of Austria.
Shiffrin, 18, the World Cup slalom champion last season, was in fourth place after her first run, but tamed the icy conditions in the second run to reach the podium.
"It turned out really well, especially since it snowed," Shiffrin said. "It was a little bit bumpy which kind of gets in your head, but if you get your skis on edge you'll arc through it."
The conditions got the better of some of the more seasoned competitors. Lara Gut of Switzerland, who is third in the overall standings, skied out on her first run and Tina Maze of Slovenia finished 14th.