The 34-year-old, still the world record holder, was excluded from the Games along with over 100 of her team mates following revelations of a systematic, state-backed doping programme in Russian sport.
Isinbayeva received 45 votes in favour and 23 against with two IOC members abstaining as she was confirmed a member of the Olympic body three days after earning a spot on the IOC's athletes' commission.
With tears in her eyes, she greeted IOC President Thomas Bach following her election. She will now serve an eight-year term on the body as a member of the commission which represents athletes' interests.
The other four athletes' commission members - Germany's Britta Heidemann, Hungary's Daniel Gyurta, Ryu Seung-min of South Korea and New Zealand's Sarah Walker - were elected with overwhelming majorities each.
None received more than three votes against them.
Isinbayeva, who announced her retirement as an athlete this week, had repeatedly criticised the international athletics' federation (IAAF), saying she would never forgive it for banning Russians from the Games.
"It is a violation of human rights. I will not be quiet, I will take steps," she had said in July. "I will go to the human rights court. I will prove to the IAAF and World Anti-Doping Agency that they made the wrong decision."
Isinbayeva, who won gold at the Athens and Beijing Games, is also hoping to replace Dmitri Shlyakhtin as head of the Russian athletics' federation (ARAF) when he steps down in November.
(Reporting by Karolos Grohmann; Editing by Brian Homewood and Ken Ferris)
