Gisin, lying third fastest after the opening downhill, kept her nerve in the slalom to clock an aggregate of 2min 20.90sec.
Shiffrin, who won the giant slalom gold here but could only finish fourth in her favoured slalom, was almost a second back, while another Swiss racer, Wendy Holdener, took bronze at 1.44sec.
Lindsey Vonn, leader in the downhill, failed to finish the slalom.
Also overnight, Switzerland's Ramon Zenhäusern took silver in the men’s slalom behind shock winner Swedish veteran Andre Myhrer as the favourites, Austrian Marcel Hirscher and Henrik Kristoffersen of Norway, both imploded.
Zenhaeusern of Switzerland won silver after coming in 0.34sec behind Myhrer, and Michael Matt of Austria the bronze.
This is huge Ramon Zenhäusern! ???
The #Swiss brings home two solid runs and wins #silver in the men's slalom race at #PyeongChang2018!#HouseofSwitzerland #HoppSwiss #Allin4PyeongChang pic.twitter.com/5xCJuBwX8n
— #HouseofSwitzerland (@HofSwitzerland) February 22, 2018