Innerhofer turned in a flawless runoff in 2 minutes, 29.82 seconds on the bumpy course, topping Austria's Klaus Kroell by 0.30 seconds and Hannes Reichelt, also of Austria, by 0.76.
"I skied like never before, I can definitely say that," said Innerhofer, who is second in the men's downhill standings behind Norway's Aksel Lund Svindal, who failed to finish his run.
"I pushed as hard as I could for as long as I could," Innerhofer said. "I think I made no mistakes but Kroell sure wasn't joking either and gave it a good shot."
Erik Guay of Canada took fourth place and Marco Sullivan was the top U.S. finisher with 13th place.
Svindal, who is second in the overall World Cup point standings, dropped a ski and took a spectacular spill into the safety net, but was not injured.