"Re-analysis of Chernova's samples from Beijing 2008 resulted in a positive test for the prohibited substance... turinabol", a type of anabolic steroid, the IOC said.
The 29-year-old had been promoted to third after the original silver medallist, Lyudmila Blonska of Ukraine, was disqualified after testing positive for steroids.
The Russian has been ordered to return her medal while the Russian Olympic Committee has been charged with ensuring the ban is implemented.
It means Briton Kelly Sotherton, who originally finished fifth in the Beijing Games, now stands to be awarded the bronze medal.
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Meanwhile, Russian 400 metre runner Maksim Dyldin has also been disqualified from the London Games after his retested sample was found to contain the same steroid as Chernova's.
Dyldin finished 17th in the 400m in London and helped Russia to fifth in the 4x400m relay -- those results have been annulled.
The International Association of Athletics Federations will now decide whether to imposed any additional punishments, such as doping bans.