Taking advantage of a tricky course set arranged by one of her coaches, Fischbacher navigated her way down Franz's Run in 1 minute, 20.14 seconds.
"It was really crazy," Fischbacher said. "It was a really straight course and you had to push from start to finish."
Tina Maze of Slovenia took a surprise silver, 0.49 seconds behind, and Vonn had to settle for bronze, 0.74 seconds back.
Many of the prerace favorites struggled with a sharp right turn midway down, but Vonn made it through that section without a problem. But then she lost nearly half a second on the bottom section.
"Once I got past those difficult sections, I kind of backed off the gas pedal," Vonn said. "I felt like I just didn't ski as aggressively as I could have, and I think that's where I lost the race."
Vonn celebrated as if she had won, raising her arms in triumph, then was relaying a course report via a two-way radio up to her teammates still at the start when Fischbacher beat her.
Fischbacher looked like she didn't believe it when she glanced at the scoreboard upon crossing the line, backing into the safety mattresses lining the finish area and nearly falling over.
Vonn won gold in the downhill to open her Olympics, then wiped out in the slalom leg of the super-combined. Depending on how her bruised right shin holds up, the American still has two events remaining at the Vancouver Games - giant slalom and slalom.
Vonn was hurt Feb. 2 during pre-Olympic practice in Austria. While other skiers were free-skiing the course Friday, Vonn took a complete day off to give her shin more time to heal.
"It's definitely sore," Vonn said. "I didn't do the free-skiing on the race hill, which all the other athletes did. Maybe I should've done that; maybe I shouldn't have. I don't really know looking back what the right decision was. It definitely gave me time to get my shin better, and that's what I need at this point."
Vonn started 17th, Fischbacher skied 19th and Maze was 22nd out of the starting gate. With the race beginning at 10 a.m. PST, most of the course was covered with shade for the earlier starters, and later skiers had better visibility.
Julia Mancuso, an American who won silver medals in her opening two events, almost went off course on a hard right turn, and finished ninth.
Mancuso was the first skier on the course and had no reference points to look for the most treacherous spots.
Fischbacher's coach, Juergen Kriechbaum, set the course according to International Ski Federation rules that rotate the job to correspond with the higher-ranked super-G skiers.
"The course up top was a lot faster than I expected," Mancuso said. "I was just carrying more speed than I anticipated into that turn. I knew when I crossed the line . . . that I blew it."
With five events remaining, the United States already has collected its most Alpine medals - seven - at a single Winter Games, topping the five at Sarajevo in 1984.