Vlhova powered down the second of her two runs under the floodlights for a combined time of 1 minute 59.05 seconds, edging out second-placed Katharina Liensberger of Austria by just five hundredths of a second.
Switzerland’s Michelle Gisin, who claimed her first slalom World Cup win in Semmering last week, completed the podium of Sunday’s event.
Shiffrin, who has only recently returned to the circuit after the unexpected death of her father Jeff last year, was seeking her fifth victory at the iconic venue, just outside the Croatian capital, but came up just short.
A fine second run boosted the American’s hopes, but first Gisin then the other podium finishers edged ahead, leaving her 0.27 seconds off the pace.
Vlhova has consolidated her lead in the overall World Cup and individual slalom standings with her 11th career victory, but acknowledged it had been a close run thing with conditions tough for the later starters on the second run.
“Today was a really tough day and in particular the second round but I found something and pushed more before the finish,” she told Eurosport.
“When I saw I was only the 11th fastest in the second run, I thought I was for sure out of the podium, but then the green light showed up and I couldn’t believe it.”
Three-time World Cup overall champion Shiffrin has been concentrating on her favored technical events since her return, claiming her 67th win in the Courchevel giant slalom last month.
Sunday’s race was her sixth in slalom without a victory, but she insisted “things are going in a good direction” in only her sixth race back following her extended break.
Shiffrin won two golds at the last world championships in 2019 but has yet to decide on whether to defend her Super-G crown at next month’s championships in Cortina, Italy, having done little specific training in the speed events.
But with the three podium finishers in Zagreb in fine form and with Shiffrin returning to her best the stage is set for a battle royal for medals in the slalom and giant slalom races at the championships.