The IAAF has put a blanket ban on the Russia team but Darya Klishina had been cleared for Rio as the governing body was satisfied she was not doping.
However, the IAAF has now revoked the long jumper's eligibility based on new - but unspecified - information.
The 25-year-old insisted: "I am a clean athlete", and said she would appeal against the decision to the Court of Arbitration for Sport.
Russian track and field athletes were banned en masse from the Olympics following claims the country ran a state-sponsored doping programme.
"I have proved that [I am clean] already many times and beyond any doubt,"Klishina wrote on her Facebook page.
"I am falling victim to those who created a system of manipulating our beautiful sport and is guilty of using it for political purposes.
"I will take every possible effort to protect my clean image."
Klishina had been cleared to compete as her drugs-testing record was established in the United States, where she is based, rather than in Russia.
She was scheduled to compete in the long jump, which begins on Tuesday.
Russian Olympic chief Alexander Zhukov, quoted by Russian news agencies, said the IAAF's last-minute suspension of the country's only track and field athlete in Rio was "a cynical mockery".