After her first run left her nearly a half second out of first, she told American television she had vomited before the start and there were concerns she may have picked up the norovirus that had plagued security staff at the Games and has now affected its first athletes.
But the 22-year-old said she felt fine and dismissed that as an excuse after the race.
"I don't feel sick right now, I don't think I have a virus," she told reporters after the race.
"I was thinking that after the first run but it might have been a little bit of me trying to make an excuse."
Shiffrin, who finished behind Sweden's Frida Hansdotter, Switzerland's Wendy Holdener and Austria's Katharina Gallhuber, said she was her own worst enemy at the Yongpyong Alpine Centre.
"The only one who can beat myself in slalom is me and I beat myself in the wrong way today," said Shiffrin.
"I know I have the best slalom turns in the world but I didn't put it out in the two runs where it mattered.
"Coming here and today and skiing the way that I did, really conservative, was a huge, huge disappointment. It's hard to explain how that feels but that's how life goes.
"It's a really big bummer but I will learn."
Shiffrin's failure to medal in the event in which she is the World Cup leader and was the 2014 Sochi winner, came as a surprise even to her competitors.
"When I went to the finish I thought, Mikaela must be in front but then I saw Frida cheering," silver medallist Holdener said.
"So there have been a lot of surprises today. But Mikaela skis that good and she will do it another time."
Shiffrin, who won the giant slalom gold on Thursday, will now get a day to recuperate as she had already decided not to compete in Saturday's super-G.
(Editing by Greg Stutchbury)
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