Holdener came from second place in the first run and clocked at one minute and 56.29 seconds, 0.47 seconds ahead of Shiffrin. Petra Vlhova from Slovakia was in the lead after the first run but ended up in third, 0.70 seconds behind Holdener.
The 29-year-old Holdener, who took her second slalom win this season, is now in second place in the overall rating with 366 points, 19 behind leader Shiffrin.
"It is amazing. I can believe it, but it is unreal I guess. My second run was the best run I showed in a race actually," Holdener said.
Shiffrin, whose second place gave her 123 career World Cup podiums, acknowledged the schedule was taking a toll on her as she is chasing her fifth overall tournament victory.
"You just have to recover the best you can. Today I am mostly happy with my performance but not completely satisfied," Shiffrin said.
Next weekend, the World Cup moves to St Moritz, Switzerland, where the women will participate in speed races.
