Vlhova is the second Slovak to win the Snow Queen Trophy after Veronika Velez-Zuzulova did so in 2017.
Last year's winner and four time Sljeme champion, American Mikaela Shiffrin, was second (+1.31), while Austrian Katharina Liensberger finished third (+3.49).
Croatia's Leona Popovic failed to make it into the second run, trailing nine hundredths of a second behind Austrian Michaela Dygruber who placed 30th.
Shiffrin leads in the overall World Cup rankings with 826 points, ahead of Vlhova with 513 points.
The men's slalom race takes place on Sunday. The first run is scheduled for 2.15 pm and the second for 5.40 pm.