The 24-year-old Austrian extended her first-leg lead to beat Viktoria Rebensburg of Germany by 0.61 seconds.
"It's just amazing. It was a fight in the second run," said Fenninger, the Olympic silver medallist in giant slalom, who had to contend with cross winds, rain and a rutted snow surface.
Jessica Lindell-Vikarby of Sweden was third, trailing 0.68 behind Fenninger's combined time of 2 minutes, 00.15 seconds, and retained her lead in the season-long GS standings.
Still, it is Fenninger who leads overall, using the 100 race points for victory to take a slender seven-point advantage — 1,151 to 1,144 — over Maria Hoefl-Riesch of Germany.
"I'm so happy that I can win two times in Are," said Fenninger, whose late-season surge has her contending for the overall title for the first time.
Hoefl-Riesch, the 2011 overall champion, had a better second run yet still placed 10th, 2.32 behind her new rival.
Marie-Michele Gagnon of Lac-Etchemin, Que., was 25th and Marie-Pier Prefontaine of St-Sauveur, Que., didn't qualify for the second run.
Five scheduled races remain this season, starting with a slalom on Saturday when the German will be favoured to regain the lead.
Hoefl-Riesch, the 2010 Olympic slalom champion, has three top-5 finishes in World Cup slaloms this season, while Fenninger has not started in the discipline since December 2011.
Fenninger also won the Olympic super-G title last month, and has two victories and a runner-up finish in three World Cup races since the Winter Games.
Rebensburg, who took a bronze medal defending her Olympic GS title in Sochi, got her best-placed finish of the season.
With one GS race remaining, Lindell-Vikarby has a 14-point lead over Fenninger in the discipline standings.
The final race closes World Cup finals week at Lenzerheide, Switzerland, on March 16.
On Saturday, new Olympic slalom champion Mikaela Shiffrin of the United States will start as favourite. She placed 24th on Friday, more than three seconds behind the winner.
American teammate Julia Mancuso placed 20th and fell outside the top-25 places in the season-long GS standings, which determines the line-up at the World Cup finals.