Defago finished in 1 minute, 10.38 seconds, 5/100ths of second ahead of Miller and 0.15 seconds faster than Max Franz of Austria and Norway's Aksel-Lund Svindal, who tied for third place.
"I was not sure my run would be fast enough to win until the very end of the race, but when I came down and I saw that I beat Bode and Aksel I knew I had a good run," Defago said.
Bad weather prompted race officials to move the starting line farther down the hill, which contributed to the close times.
"It was pretty basic," Miller said. "Ski racing is all about making do with what you get with weather. This super-G here didn't give us a lot of chances to make up time."
Sharing the podium with Franz helped Svindal cement his lead in the overall World Cup point standings. The Norwegian veteran placed second in the downhill Saturday.