The 27-year-old completed the course at Bad Kleinkirchheim in one minute 9.80 seconds to pip Lara Gut by 0.18 seconds, leaving the Swiss waiting for her first win since suffering a knee injury last February.
The organizers postponed the downhill which was supposed to be held on Saturday and brought forward the Super G after heavy rain earlier in the week damaged the course. The downhill will now be held on Sunday.
Most skiers struggled in the conditions, including four-times overall World Cup winner Lindsey Vonn who finished ninth, however Brignone said she relished them.
"When the race is tough, I'm better," she told Swiss broadcaster SRF after winning her second race of the season following her giant slalom win in Lienz in December.
"These are my conditions because it's all in the head and you have to attack."
"I did everything I expected and in this Super G you must know what you have to do in the right place. Everyone else made mistakes and I didn't."
Gut was runner-up for the second time in a World Cup race following her comeback from the knee injury she suffered at the world championships in St Moritz last February, when she tore her anterior cruciate ligament.
She might have won but for a mistake at the end of the course when she hit a gate with her arm, costing her crucial tenths of a second.
American Mikaela Shiffrin, a slalom specialist who holds a huge lead in the overall World Cup race, did not take part. The 22-year-old heads the overall standings with 1381 points, an almost insurmountable 821 clear of Swiss Wendy Holdener.
(Writing by Brian Homewood in Wengen, Switzerland; Editing by Ken Ferris)
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