Rast ends Shiffrin slalom streak to claim Kranjska Gora double
Shiffrin had been looking to extend her slalom run having won all five races in the discipline this season, in addition to last year's season-ender.
But the overall World Cup and slalom leader had to settle for second place 0.14 seconds behind Rast.
The Swiss skier and her compatriots wore black armbands to pay tribute to the victims of the New Year's Eve bar tragedy at Crans-Montana.
And the reigning slalom world champion blitzed to the fastest time in both runs having also led Shiffrin by 0.10sec after the first run.
"I gave it everything I had this weekend," said Rast, who achieved the fourth World Cup victory of her career and a fifth podium in as many races.
"Achieving the double was extraordinary.
"I think a lot of energy (was the key). It was a big battle, my energy made the difference, the preparation was perfect.
Rast looks to have recovered from the hip problems that had plagued her since last season just over a month before the Winter Olympics get underway in Milan-Cortina.
Swiss skier Wendy Holdener completed the podium at 1.83sec.
Shiffrin dominates the overall World Cup standings with 823 points, 120 points ahead of Rast.
The American also leads the slalom standings with 580 points, 218 points ahead of Rast.