Fenninger finished 0.71 seconds ahead of Nadia Fanchini of Italy and 1.07 faster than fellow Austrian Eva-Maria Brem after two powerful runs in Are, the penultimate stop on the World Cup circuit.
The result means Fenninger bumps Tina Maze — who finished 20th after a disappointing second run — from the top of the overall standings.
Marie-Pier Prefontaine of Mont-Saint-Sauveur, Que., was the top Canadian in 26th.
Fenninger trailed Maze by more than 300 points a few weeks before last month's world championships in Colorado but reduced the deficit race by race. Last year the Austrian was in a similar situation, reducing a big deficit to Maria Hoefl-Riesch before winning by 191 points.
"It's like a deja-vu," Fenninger said. "Last season when I left Are I was in the lead and now it's the same."
However, Maze has a chance to reclaim the overall lead in the slalom on Saturday, when Fenninger won't be competing.
Fanchini was a big surprise in second place — her first podium finish since 2010 and first ever in giant slalom. Brem's third place means she stays in contention to challenge Fenninger for the World Cup crystal globe in giant slalom, with one race remaining.
"It's nice to have a chance. It's over when it's over," Brem said.
Mikaela Shiffrin, who turned 20 on Friday, missed the podium by 0.02 seconds and finished fourth. Despite improving from sixth after the first run, the American slalom specialist was disappointed she didn't take as many risks as Fenninger.
"She has impeccable technique and seems like no fear," Shiffrin said of the Austrian. "I feel like she's the only one who deserves to win GS's right now."