The double Olympic champion records her 43rd slalom and 64th overall World Cup win with victory on Austrian slopes.
Shiffrin had skipped the previous World Cup stop in Val d'Isère, France, to focus on the races in Lienz after a disappointing 17th in the giant slalom at Courchevel.
Both Vlhova and Shiffrin drew early starts, with Vlhova second down the piste on the first run.
A solid run saw the Slovak cross the finish line in 54.80 seconds, and when Shiffrin took to the course immediately after she found herself behind Vlhova at all three timing intervals.
However, the double Olympic champion and four-time reigning slalom world champion gained plenty of time in the final sector, coming from 0.01s behind Vlhova at the third intermediate point to cross the line in 54.54 seconds, 0.26s ahead.
None of the remaining skiers were able to match either woman, with Nina Haver-Loeseth the closest at 0.70s behind Shiffrin.
Multiple errors on her second run cost Haver-Loeseth a spot on the podium with the Norwegian eventually finishing down in 19th.
Gisin, who beat Shiffrin for gold in the combined at PyeongChang, secured her World Cup podium finish in just over 12 months and the first World Cup slalom podium of her career.
Vlhova's second run was not perfectly clean but she was calm and collected, keeping her nerve to put over a second between her and Gisin to better her third place in the Lienz slalom in 2015.
Shiffrin lost time on Vlhova at the start of the second run, but the American - wearing the red bib as the current slalom standings leader - was flawless after that.
She made up time all the way to the finish to win by 0.61 seconds and claim her extend her World Cup slalom win tally to 43.