In Saturday's super-G in the Tyrol, Brignone became the first Italian woman to win 21 races in the women's elite alpine skiing competition.
Gut-Behrami was in third but 24 hours later she came out on top from a trio of Italians led by Brignone, 15 hundredths of a second adrift.
Marta Bassino completed the podium.
This was Gut-Behrami's 36th World Cup win and second this season after her giant slalom success in Killington in November.
Brignone's profitable weekend at St. Anton lifted her to the top of the discipline standings.
Missing from the super-G show in St Anton was Mikaela Shiffrin, who has a healthy lead in the overall standings, and Italy's Sofia Goggia, who sat out the race "as a precaution" after a crash on Saturday, with next week's speed races at home in Cortina d'Ampezzo.
Unlike Saturday, when the route had been shortened because of high wind, the skiers descended the Karl Schranz piste on a complete course under grey skies.
Gut-Behrami's run was far from perfect with her right ski in the air at one point on the full-length top section, and almost came a cropper following the jump into the Eisfall.
But she recovered impressively to post the best combined time in the last two sectors.
"It didn't really go as planned," said the world super-G champion of the difficult piste which 17 of the 45 starters failed to finish.
"St. Anton is a tough race, it's a really interesting slope.
"On the flat part I made a lot of mistakes and I never expected to be that fast," she said.
"The last part I tried to ski clean and let the ski go. I'm not so happy with the top (section) but I'm happy with the result."
At 31, she collected her 18th victory on the world circuit in the discipline, placing her second all-time behind American Lindsey Vonn's 28.
"I'm happy to be skiing at this level in super-G after so many years," she said. "My first victory in super-G I had it 14 years ago, I never thought I would have so much success."
Brignone drifted wide before the entry to the Eisfall to lose momentum before recovering with a brilliant bottom section.
"I had this big mistake before Eisfall and I was really stuck before the steep and I lost a lot of time. I'm sorry because like yesterday I made up time (on the bottom section)," Brignone said.
"Today I was really good but not as good as yesterday — but that's OK, I'm really happy about my weekend."
Newt week's races in Cortina d'Ampezzo will feature one super-G race and two downhills, including the one cancelled in St. Anton this weekend, the International Ski Federation (FIS) announced.
