Vlhova, who lifted the world title in Are in February, set the pace with a blistering first run of 1:12.59.
'Magical!' - Vlhova leads Giant Slalom after bottom-section brilliance
Shiffrin: I wanted to ski with risks today
09/03/2019 AT 13:34
By contrast Shiffrin really struggled to find her groove and finished over a second off her rival going into the second run.
However the American took things up a notch in her second run as she flew down the track to finish with a total time of 2:25.29, with second run time of 1:11.37, the fastest of any racer.
'What a ski!' - Shiffrin screams in delight after superb second run in Giant Slalom
It was only enough for bronze though as Vlhova and Germany’s Viktoria Rebensburg did more than enough to consolidate their top two positions, an exact repeat of the World Championships.
Vlhova pips Rebensburg to victory in Giant Slalom
It is Slovakian Vlhova’s second outright Giant Slalom victory of the season and it moves the 23-year-old into second in the standings.
Yet she is still 97 World Cup points behind Shiffrin, who will expect to win the Giant Slalom in the final meet of the season Soldeu next Sunday.
Vlhova was easily the favourite for the home crowd and she paid tribute to those supporters.
“Every day I am much better in Giant Slalom but everything is inside me and we did a lot of hard work with my team
I’m really happy that I could win today because it is in Czech Republic and is really close to Slovakia so I had a lot of fans here and it’s just amazing.
Great Britain’s Alex Tilley was another to really find her feet in the second run as she improved her time to finish in 28th.
Spindleruv Mlyn slalom: Wendy Holdener's second run
09/03/2019 AT 13:28
'What a run!' - See how Shiffrin set new World Cup record in Spindleruv Mlyn slalom
09/03/2019 AT 13:25