The 2022 Olympic slalom gold medallist slipped at the ninth gate in the icy first leg and was pitched into the safety netting.
The technical specialist, still second in the overall standings behind American Shiffrin, was taken off the piste by sled and flown to hospital by helicopter.
"Petra has damaged ligaments in her knee and the season for her has ended," the Slovak Ski Association said in a statement.
The official website quoted Vlhova thanking her fans for their support.
"I am positive I can handle the situation. I will fight for the earliest possible comeback," she added.
Vlhova won the 2021 overall World Cup and was the giant slalom world champion in 2019.
She is the third top Alpine skier to be airlifted to hospital due to a fall this month, after France's Alexis Pinturault and Norway's Aleksander Kilde.
Reigning Olympic giant slalom champion Sara Hector of Sweden won the race, 1.52 seconds ahead of Shiffrin, who chalked up her 149th World Cup podium, and New Zealand's Alice Robinson.
The win was Hector's first in the discipline for nearly two years.
The women ski a slalom on Sunday.
Shiffrin leads the overall standings with 1,109 points to Vlhova's 802 and Swiss skier Lara Gut-Behrami on 789.
Vlhova was also Shiffrin's main rival in slalom, with the American only 25 points clear of the Slovak.
