Innerhofer covered the 2.18-kilometre course in 1 minute, 9.17 seconds, ahead of Calgary's Jan Hudec and Max Franz of Austria.
Eric Guay of Mont-Tremblant, Que., was seventh. He won the downhill in Garmisch two years ago and was second in last year's World Cup race. He also clinched the super-G World Cup title by winning the final race in 2010 on this course.
Fresh snow and fog forced organizers to shorten the course to a super-G length for the second straight day.
Hudec was 0.33 seconds behind and Franz 0.36 back. The top 15 finishers all finished within a second of each other.
Innerhofer failed to win a medal at the recent world championships in Schaldming, Austria. But he won three medals when the worlds were held in Garmisch-Partenkirchen two years ago — gold in the super-G, silver in the super-combined and bronze in the downhill.
He also shared fourth place in last year's downhill at the German resort.
Another Italian, Werner Heel, was fourth, ahead of Steven Nyman of the United States.
Aksel Lund Svindal of Norway, the downhill gold medallist from Schladming, shared 26th place in training.