"Re-analysis of Kapachinskaya’s samples from Beijing 2008 resulted in a positive test for the prohibited substances stanozolol and dehydrochlormethyltestosterone (turinabol)," the IOC said.
Jamaica were third and Belarus finished in fourth place in the Beijing race.
"The IAAF (international athletics federation) is requested to modify the results of the above-mentioned events accordingly and to consider any further action within its own competence," the IOC said.
Kapachinskaya was also disqualified from her 400m run where she had placed fifth.
Her Russian team mates Alexander Pogorelov, who was fourth in the decathlon, and shotputter Ivan Yushkov also had their Beijing Games results cancelled out after testing positive for the same substance.
Yushkov was 10th in his event eight years ago.
Earlier this week Russia were ordered to return their gold medals from the 4x100m women's relay from the same Games after Yulia Chermoshanskaya also tested positive in a re-test.
The IOC stores samples for a decade to test with newer methods or for new substances. The ruling body conducted targeted re-tests before the Rio Olympics.
A total of 98 samples were positive in reanalysis of samples from both the Beijing Games and the 2012 London Olympics as the IOC attempted to root out cheats and stop them from going to the Rio Games.
Russia's track and field team, with the exception of one athlete based in the United States, were banned from the Rio Games over what the World Anti-Doping Agency (WADA) said was a state-backed doping programme.
(Editing by Clare Fallon)
