The reigning World Cup overall champion led Mikaela Shiffrin by 0.18s after the first leg.
Despite a huge error on the top half of the second run, the American managed to go top of the time sheets with just Vlhova to go.
But the Slovakian ace was simply flawless, posting the quickest time on both legs for the second day in succession to win by 0.47s.
Vlhova's win saw her become the most successful skier in history at Levi with one more triumph than Shiffrin's tally of four.
The pair are now level on 260 points at the top of the overall World Cup standings with Slovenia's Andreja Slokar 76 points back in third and Duerr a further 28 points behind in fourth.
Speaking in her post-race interview, Vlhova said, "It was so difficult today because, honestly, I didn't like too much the second run so it was a big fight. But I did it.
"I want to say thanks to my coach, to my team, to my family, because without them I am maybe not sitting here. I don't know... I'm really happy."