Vlhova clocked 51.30 seconds in the tightly-gated opening run before following up with 56.32sec in the second.
The Slovakian put half a second on Lena Duerr in the second run with the German finishing 0.72sec behind.
Leona Popovic was third after the first run but a mistake halfway down the second knocked the Croat out of contention and allowed the American AJ Hurt to claim her first World Cup podium.
The 23-year-old Californian, who made her World Cup debut in 2018 when she was just 17, was 16th fastest on the first run, over two seconds behind Vlhova, but pulled out the fastest run second time around to finish 0.87sec behind the Slovakian.
Her teammate Shiffrin, however, endured a poor weekend.
Having finished only ninth in Saturday's giant slalom, her worst result in the discipline since November 2022, the five-time World Cup overall winner straddled a gate in the second sector and failed to finish, ruling her out of the second run.
It is the first time since the Beijing Winter Olympics in February 2022 that Shiffrin has gone out in her favourite event - 56 of her 93 World Cup victories have come in the discipline.
Vlhova is now just five points behind Shiffrin in the discipline standings but remains 207 behind the American in the overall, although she has jumped past Federica Brignone into second.
