Dubbed "Winnerhofer" when he won the Super-G world title in Garmisch-Partenkirchen two years ago, Innerhofer lived up to his nickname by taking victory in one minute and 37.83 seconds,
On a course he relishes, the Italian followed up wins at Beaver Creek and Wengen by finishing 0.12 ahead of Georg Streitberger.
Klaus Kroell was 0.16 off the pace, followed by Hannes Reichelt and Norway's world champion Aksel Lund Svindal.
Innerhofer, who also won a downhill bronze medal on the same piste in 2011, took advantage of his knowledge of the terrain and improving visibility conditions to bag the sixth World Cup laurels of his career.
The battle for the discipline's crystal globe is extremely tight with two races left.
Svindal is on 359 points, 10 ahead of Italy's Dominik Paris and 15 ahead of Innerhofer, who lost vital points when he was forced to start the Kitzbuehel downhill in 46th position after ignoring a yellow flag in practice.
The men's programme continues in Garmisch-Partenkirchen on Sunday with a giant slalom.