Alexis Pinturault of France finished second, 0.35 seconds behind, and Ligety, the American who won by a massive margin last year, was 0.41 back.
"I'm happy to see that Ted is beatable and human," said Hirscher, adding that a small change he made in his setup three days ago made a big difference.
"We worked really hard over the past year and sometimes we didn't know if we were doing exactly the right thing. There are so many different (variables)," Hirscher said. "At the end it was just a small screw in my setup. ... That helped me in the turns and to drift less."
Not surprisingly, Hirscher would not provide more details about the screw or where exactly it was located.
Ligety struggled with the soft conditions a sharp change from past seasons when the Gran Risa was extremely icy and dropped 60 points behind Hirscher in the giant slalom standings.
"I'm happy with third," Ligety said. "I don't feel like I skied my best but that's not easy to do every time."
Having won the opening two GS races of the season, Ligety failed to complete two events in Val d'Isere last weekend then also skied out in Friday's super-G in Val Gardena.
"I've had a tough European trip and it's nice to put in a decent result," said Ligety, who will head home Tuesday for a brief break. "It's not been an easy December for me."
Considered one of the circuit's top giant slaloms, the Gran Risa begins with a steep and twisty section through the trees then flattens out with a series of rolls before the finish, meaning it's tough to make up time if any mistakes are made in the first half of the course.
"It was just so easy and grippy that I definitely didn't have quite the right approach and just was thinking it was going to be slicker than it was," Ligety said after also finishing third in the opening run. "I had a couple of those little mistakes and you pay hard on this type of snow.
Another factor in his victory, Hirscher said, was pre-dawn testing on race day.
"We were up at the top at 7 a.m. today using head lamps," he said. "We were the only ones up there. It was crazy but in the end it was a good decision.
"We have to work further on these things we learned over the last few days, and hopefully get better and better and better," Hirscher said. "Ted will be really stronger in the next race for sure, because now he knows the rest of the world is getting close to him."
Another American, Tim Jitloff, finished fifth to match his career best result from Sestriere four years ago.
"I just felt like I was on and I was doing it right," said Jitloff, who started with the No. 31 bib. "To come to the place that is the definition of giant slalom racing and throw down a fifth, I couldn't be happier."
Overall World Cup leader Aksel Lund Svindal was 13th and maintains a 95-point lead over Hirscher in the standings.
Bode Miller failed to advance from the first run, which he finished in 40th.
Miller fell on his hip midway down, recovered, but then stood up out of a tuck before he concluded a wild run.
Miller ruined his race skis in a crash last weekend and with his wife, Morgan, and son accompanying him in Europe, he didn't find the time this week to test new ones.
"I was just telling Morgan, it's not her fault or Nate's fault but I don't spend nearly the time thinking about skiing that I did in the past," said Miller, whose best result this season was second behind Ligety in a GS in Colorado earlier this month. "And I keep making really stupid mistakes."
After Christmas, the circuit resumes with a downhill in Bormio, Italy next Sunday. Several top racers including Ligety and Miller will compete Monday in the Alpine Rockfest, an exhibition event at the Paganella resort in Andalo.
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