The meeting on Wednesday was called after he admitted to having sex with a junior staff member at the federation’s headquarters in January.
The Mail & Guardian has learnt that the junior staff member has also been put on special leave.
Both Vavi and the staff member will face a disciplinary hearing to be headed by an independent person.
Vavi is likely to be charged with bringing the organisation into disrepute and hiring the junior staffer without following proper protocol and having sex with her at the Cosatu offices.
Attempts by Vavi’s supporters, including the National Union of Metalworkers of South Africa (Numsa) and the Food and Allied Workers' Union (Fawu), to cancel the sitting of the special central executive committee, which they claimed to be unconstitutional, failed. The two unions also unsuccessfully argued that Cosatu needed to take the mandate from its members before the decision to suspend Vavi was effected.
According to Cosatu insiders, Vavi was asked to leave the meeting at around 2pm on Wednesday after the report of the previous commission of inquiry was presented.
The report recommended that Cosatu should take action against Vavi as the federation had a strong case against him.
"The chair of the previous inquiry said we had a strong case against Zweli. We agreed that both needed counselling and that the federation should support them for trauma. They have families," said a Cosatu insider.
"The meeting was tense and tough but we managed to keep cool heads. We requested him to leave the meeting. Before he left he admitted to his mistakes and asked for an apology. The [central executive committee] did not respond to him while he was there. We asked him to leave so that we can discuss the report."
Cosatu’s deputy general secretary Bheki Ntshalintshali will act in Vavi’s position.
Vavi's supporters believe his enemies are using the sex scandal to remove him from Cosatu because of his critical views on President Jacob Zuma and his administration.