"Vavi has been released from all his official duties as the general secretary (of COSATU) during the period of investigation until such time that the outcome of the disciplinary hearing is known," reported Xinhua quoting party's deputy general secretary Bheki Ntshalintshali as saying.
As the largest of the country's three main trade union federations with 1.8 million workers, the COSATU is part of the tripartite alliance with the African National Congress and the South African Communist Party in ruling the country.
Last month a junior COSATU employee accused Vavi of rape, but he said that he had a consensual affair with her.
The central executive committee (CEC) of the COSATU Wednesday met in Johannesburg to discuss the possible disciplinary action against him.
"After lengthy discussion, the CEC meeting agreed to conduct a full investigation into the allegations," COSATU president Sidumo Dlamini said Thursday.
Photos: Katrina Kaif, Shamita Shetty at Mumbai airport
Photos: Varun Dhawan, Alia Bhatt promote 'Badri...' on 'Dil Hai Hindustani'
In pictures: 15 facts about kissing that will surprise you
Photos: Shahid Kapoor and Mira Rajput at cafe in Bandra
Photos: Deepika Padukone, Neha Dhupia and Soha Ali Khan at event