Shiffrin took a wide 0.90 lead after the first run in the wet snow of Flachau and then held off the hard-charging Swede for a combined-run time of 1 minute, 45.83 seconds.
Sweden's Maria Pietilae-Holmner placed third with a 1:46.97. Maria Hoefl-Riesch of Germany, the overall women's World Cup points leader, took fourth with a 1:47.23.
Shiffrin, 18, won the seventh championship of her young World Cup career and raised her profile further on the U.S. team that is headed for the Winter Olympics without injured Lindsey Vonn.
"It's nice to sing my national anthem a couple of races before the Olympics," said Shiffrin. "I hope I can sing it again in Sochi."
Flachau was also another highlight for the Swedish women, who have been appearing on the World Cup podium in the slalom events on a regular basis.
"It is so sweet to be part of such a good and strong team," Pietilae-Holmner said. "We train really hard together, help and push each other."