Having opened the defence of her slalom World Cup title with victory on Saturday, the Slovak has now won five consecutive rounds in her favourite discipline.
Vlhova was tied for the lead with reigning Olympic combined champion Michelle Gisin after the first run, but skied superbly on the second run to beat the Austrian into second place.
Double Olympic champion Shiffrin was second on Saturday, but struggled on the middle section of the second run having been fourth after the first run.
"I am so so happy that I can manage myself and put in all my power. At the end, it's two victories in two days so it's amazing." - Petra Vlhova to FIS Alpine
Vlhova doubles up to win third reindeer
Going first on the first run, Vlhova set the target by clocking 54.32s.
That soon turned out to be a strong performance as Shiffrin - on the course set by her coach Mike Day - crossed the line 0.37s down to leave her in third place at the time behind Vlhova and Holdener.
Then came Gisin who skied the bottom half of the course superbly to tie Vlhova for the lead, celebrating gleefully after crossing the line.
The top four were unchanged after that but, in marked contrast to yesterday when Vlhova, Shiffrin and Liensberger were well clear of the rest, there was less than a second between the top 10 after the first run.
The second run was far more challenging with those who carried speed through the top struggling on the tight turns halfway down the course.
Sixth after the first run, Liensberger skied the top conservatively before making up time on the middle section and posting an aggregate mark of 1:49.55.
Shiffrin did not take those turns nearly as well and went into second with three skiers to come.
Holdener also toiled on the bottom half of the course, but moved ahead of her American rival into second.
Then came Vlhova who was quick on the top half and managed to take that speed to the bottom, recording a time just seven-hundredths outside Liensberger's to take the lead by half a second.
Gisin was last to go and lost time at the top, but skied well on the bottom half to take second place for her best ever slalom World Cup finish.
It was Vlhova's third victory at Levi which means she is now the proud owner of three reindeer - the unique trophy for race winners at the Finnish resort.
The skiers now head to Lech Zuers in Austria for the first Parallel competition of the new season on Thursday.