Zwelinzima Vavi was last night suspended as Cosatu's general secretary.
The decision was taken at a heated central executive committee meeting that lasted several hours.
The Times has established that Cosatu will institute a full inquiry into Vavi's sexual liaison with a junior married female staff member in her office.
The probe will also look into how the female staff member, who has dropped a rape charge against Vavi, came to be employed.
Sources close to Vavi said he was "devastated".
They said the decision to suspend him would test Cosatu at all levels. There are fears that his supporters will be hounded out of the union federation.
Vavi's suspension comes a day after a staunch supporter, SA Democratic Teachers Union president Thobile Ntola, was also suspended - in what was seen as a tactical move ahead of last night's meeting.
‘I profusely apologise’
Meanwhile, Vavi took to social networking site Twitter to thank people for their support.
"I committed an error & have profusely apologised to everyone hurt by my indiscretion. That was a right thing to do," he wrote.
"I am relieved so many have accepted that apology and recognise that some remain unforgiving. Know others celebrating and rubbing salt."
In a third tweet he wrote: "Thank you for the support - will say more later." Source: Sunday Times