In two minutes 29.82 seconds, the super-G world champion won the fifth Alpine ski World Cup race of his career and the third downhill, two months after his return to the top in Beaver Creek.
Already fastest in Friday's downhill leg of the super-combined here, the Italian emulated his compatriot Kristian Ghedina who won the race in 1997, his second Wengen victory.
"If I could have picked two downhills I would have loved to win in my career, it would probably have been Wengen and Beaver Creek. To win them both in the same year is just amazing," said the 28-year-old Innerhofer.
"Ghedina's name was on the roll of honour of both races as the last Italian to win them. Now it's mine. It's obviously a great morale booster ahead of Kitzbuehel and the world championships in Schladming (from February 5-17)," he added.
Innerhofer was one of the leading lights of the 2011 worlds in Garmisch-Partenkirchen where he won the super-G and finished third in the downhill but later suffered concussion after a crash and struggled to return to his best.
On Saturday, Innerhofer beat two Austrians, 2011 winner Klaus Kroell, who was 0.30 adrift, and Hannes Reichelt, who trailed the Italian by 0.76.
Frenchman Johan Clarey was quickest in the Hanneggschuss, the fastest section on the men's circuit, and set an unofficial speed record in a men's World Cup race of 161.9 kph but had to be content with fifth place at the finish.
Norway's Aksel Lund Svindal, the downhill World Cup leader, crashed after losing a ski shortly after a jump and ended up in the safety nets.
The Norwegian was unhurt but lost precious ground in the overall World Cup, still led by Austria's Marcel Hirscher, the arch-favourite in Sunday's slalom at this Swiss resort.
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