The 25-year-old three-time world champion – who opted not to defend her multi-event Olympic title – finished 20th in triple jump qualifying on Friday, with a best of 13.97 metres.
Klüft will seek consolation in the long jump, an event in which she finished 11th in the 2004 Olympics.
Cuba’s Yargelis Savigne led the 12 triple jump qualifiers with 14.99m.