The seemingly unstoppable American had led by 0.67 seconds after the first run but, last out of the start hut, ended up second and 0.06 slower than Duerr with only the 14th best time on the second leg.
Croatia's Zrinka Ljutic was third, taking her first World Cup podium at the age of 19.
Four-times overall World Cup winner Shiffrin will now have to wait until March to equal the record, with the world championships starting on February 6 in the French Alps.
The American's 83rd win in the Italian resort of Kronplatz on Tuesday sent her clear of retired compatriot Lindsey Vonn as the female skier with most World Cup wins and she had been bidding for a fourth in the space of a week.
Sweden's Ingemar Stenmark won his 86 races in the 1970s and 1980s, with the first a slalom at the Italian resort of Madonna di Campiglio in 1974 and the final victory in a giant slalom at Aspen in 1989.
"I'm a little tired today, I wasn't sure if I could hold it over the whole course," Shiffrin had said after the first run.
"I'm just trying to focus about the simple things, thinking about the skiing ... there's so much that can still happen, I'm not really focused on the record even though yesterday evening I did have some time to think about it."
