The Olympic slalom champion had been warned by German team doctors not to compete at the Finnish resort because of a hip problem, but she ignored the advice to triumph in a combined time of one minute, 55.58 seconds.
"The injury improved in the last few days and I hardly felt anything," Hoefl-Riesch said.
"It's a bit surprising because I didn't do so well on the flat section and I really had to push it in the finish wall. I'm glad I managed to push my limits."
Saturday's result would have brought back joyous memories for the 27-year-old from Garmisch, as she won her first slalom in Levi eight years ago and also triumphed on the same course in 2010.
She eclipsed first-leg pace setter and local favourite Tanja Poutiainen by 0.55 seconds. American Mikaela Shiffrin, 17, was third, 0.74 adrift.
"It's a piste I like a lot and I think I've been on the podium each time I raced here except in 2006," Hoefl-Riesch said.
She had considered retiring during the summer break but decided against it so she can compete at the 2014 Sochi Olympics.
Poutiainen said meeting the challenge of up-and-coming skiers such as Shiffrin had become a motivation.
"It's a real challenge to fight against girls who are 15 years younger than you are," the Finn said. "They have the rage while we have the experience, and it's good for skiing to see young talent like this."
Pre-race favourite Marlies Schild of Austria missed her chance to equal the record number of 34 slalom wins held by Swiss Vreni Schneider when she straddled a gate in the morning run.
"I don't know what happened, I suddenly had a blank and I was out," the world champion said.
But Hoefl-Riesch warned that Schild would be the one to beat in Aspen later this month: "The Aspen course is very technical and it will suit Schild ideally. It will be an exciting challenge."
American World Cup holder Lindsey Vonn shunned the Levi weekend to save energy for races at home in Aspen later this month.
Winner of the opening giant slalom in Soelden two weeks ago, Slovenia's Tina Maze finished fourth to increase her lead in the overall World Cup standings to 150 points. She leads Hoefl-Riesch by 26 points while Vonn has yet to score.