This comes amid fresh sexual harassment allegations against him.
The Sowetan this week reported that Vavi had been given a warning following an incident involving a cleaner who worked for the National Union of Metalworkers of SA (Numsa).
The report said the woman lodged a sexual harassment complaint against Vavi almost a year ago after an alleged sequence of unsavoury requests by the labour federation head which involved him asking her to massage his legs and feet as well as him trying to kiss her.
On Friday Vavi said the allegations were baseless. “There is a record which that article selectively quotes where the alleged victim accepted there was a misunderstanding between her and myself and the matter was closed after she twice refused to take it forward,” he said.
Five years ago reports surfaced against Vavi, former general secretary of Cosatu, in which he was accused of having an affair with a married junior employee. Those charges were withdrawn.
He said there were efforts to discredit him.
On Friday Saftu said in a statement that the recent matter had been laid to rest and " justice was served" after the complainant said she was satisfied with how the matter had been resolved.
"For the record it is true that a Numsa staff member expressed her discomfort and made allegations that (Vavi) made unwanted sexual advances and or handled her inappropriately. The allegations were made during September 2017.
"On the same day these allegations were brought to the attention of the Saftu National Office Bearers, they acted swiftly. Numsa and Saftu provided, at a senior level, an opportunity to the complainant to express herself and advise how she wished to see the matter handled," the statement said.
"Vavi was also separately approached for his version. He denied the allegations."
Saftu said that the complainant advised that she requested a formal apology from Vavi to settle the matter.
"It was her desire to have the matter settled informally, and kept confidential. To this end, both parties agreed in writing that there had been a misunderstanding between themselves. The complainant accepted and was satisfied with the intervention and twice stated that she did not wish to take the matter any further."
"Saftu is satisfied that this matter was handled fairly, with the best interests of the complainant at the heart of the chosen process. In our view justice was served."