Miller-Uibo, the 2016 and 2020 400m gold medallist who was chasing a hat-trick of Olympic titles in Paris, was aiming to seal qualification at the Bahamas trials.
However, the 30-year-old was injured ahead of the 400m final, meaning she will miss out on a place in her specialist event.
"She's the darling of the sport and she will be missed. Unfortunately she's been dinged up with some injuries," Bahamas Association of Athletic Associations (BAAA) president Drumeco Archer told Eye Witness News Bahamas.
Archer said Miller-Uibo may yet compete in Paris as part of the Bahamas' 4x400m mixed relay squad, after helping the team qualify at the world relays earlier this year.
"She's golden in our minds, and there could be some consideration for her running the relay depending on the time of her recovery," Archer said. "So we'll wait and see what happens."
Miller-Uibo has not run in an individual 400m this season.
Miller-Uibo's absence from the 400m in Paris makes her the latest Olympic athletics champion who will be unable to defend their title.
Jamaica's reigning 100m and 200m champion Elaine Thompson-Herah was ruled out of the Games through injury this week, while 800m champion Athing Mu fell during US trials in Eugene this week and failed to qualify.
