The double world champion, who now competes under the name Beloborodova, had already been banned by the International Association of Athletics Federations (IAAF) for doping earlier this year.
She won world titles in 2011 and 2013 to add to her Olympic gold but did not compete at the Rio Games due to a track and field ban on Russian athletes over doping.
The IOC ordered the IAAF to modify the results of the event in London, where Poland's Anita Wlodarczyk finished second behind Lysenko and Germany's Betty Heidler came third.
China's Zhang Wenxiu was fourth and could now be upgraded to the bronze medal.
Lysenko, 33, also served a two-year ban from 2007-09 for using steroids, missing the 2008 Olympics, and now faces a lifetime suspension from the sport.
Russia has been stripped of several medals due to re-tests from the 2008 Beijing Games and London 2012.
Among others they have lost are the women's 4x400 and 4x100 metres relay medals from Beijing as well as the women's high jump bronze from those Games.
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 from the 2008 and 2012 Games as the IOC attempted to root out cheats and stop them from going to the Rio Games.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
