Innerhofer covered the challenging Kandahar course at Garmisch in 1 minute, 38.31 seconds for his first career win in the super G.
Austria's Hannes Reichelt came in at 1:38.91 and World Cup overall points leader Ivica Kostelic of Croatia won the bronze. Didier Cuche of Switzerland placed fourth.
Bode Miller was the top American in the event. He placed 12th among the 30 contestants after losing a pole at one gate and then his balance near the finish line.
"It was bumpy enough and fast enough that it was challenging," Miller said. "You see a lot of guys making mistakes, but then you see a guy like Innerhofer ski that way and he deserves to win it. He was one of the only guys that was really pushing and taking some risk."
American Ted Ligety failed to complete the first run. Tommy Ford and Travis Ganong finished 14th and 18th respectively.