In the last slalom before the Pyeongchang Olympics, Shiffrin was quickest on the first leg and was nearly one second inside Vlhova's time on the second when she lost her balance and missed a gate within sight of the finish.
Shiffrin also failed to finish the Super G at Cortina one week earlier and the giant slalom at Kronplatz on Tuesday. She was a modest seventh in Saturday's giant slalom at Lenzerheide.
Vlhova completed her two runs in a combined time of one minute 50.53 seconds to win by one tenth of a second from Sweden's Frida Hansdotter and claim the fourth World Cup win of her career. Swiss Wendy Holdener was third.
'I’m trying to decide' - Shiffrin to make Winter Olympics decision
Shiffrin is widely expected to retain the Olympic slalom title she won at the 2014 Games in Sochi, as well as having a shot at gold medals in the giant slalom and Super G.
Although Shiffrin has won 10 World Cup races this season and is runaway leader in the overall standings, she has suffered a dip in form in the run-up to Pyeongchang.
World Cup wrap: New era finally here after season where anything was possible
Robinson's sizzling run denies Shiffrin in final giant slalom of season