The 19-year-old Shiffrin, who is based in Eagle-Vail, Colo., won her third U.S. title overall, after slalom championships in 2011 and 2012.
She completed Thursday's two runs in 2 minutes, 30.93 seconds. The race was open to women from other countries, and Marie-Michelle Gagnon of Canada finished second, 1.88 seconds behind.
Julia Mancuso, a four-time Olympic medalist who lives in Squaw Valley, was third.
Shiffrin became the youngest slalom champion in Olympic history last month at the Sochi Games, then returned to the World Cup circuit to wrap up a second consecutive slalom season title.
All nine of her World Cup career race wins have come in slalom.