"I have instructed my lawyers to challenge the decision to put me on leave of absence pending investigation and possible disciplinary action," he said on Friday.
"I believe a grave injustice is being visited on me. I believe that my suspension will be proven to be both procedurally and unsubstantially unfair.
"The laws of the country, including the right to be treated fairly, has been trampled upon by the very same people who are mandated to defend the rights of workers and all South Africans, including myself."
He said one of the reasons he was challenging the suspension was that Cosatu president Sidumo Dlamini had circulated an "intelligence report" that aimed to "destroy" him.
Cosatu announced on Thursday that Vavi had been put on special leave pending the outcome of a disciplinary hearing relating to an affair he had with a junior Cosatu employee.
"[Vavi] has been released from all his official duties as the general secretary during this period of investigation until such a time that the outcome of the [disciplinary] hearing is known," deputy general secretary Bheki Ntshalintshali said.
Dlamini said Vavi was placed on special leave after the special central executive committee meeting.
Last month, a junior Cosatu employee accused Vavi of rape. He admitted to having a consensual affair with her.
The woman subsequently withdrew a sexual harassment complaint against him.
Vavi said the intelligence report, which he distributed at the briefing, aimed to discredit a number of South Africans including ANC MP Tokyo Sexwale, deputy chief justice Dikgang Moseneke, ANC deputy president Cyril Ramaphosa and National Union of Metalworkers of South African general secretary Irvin Jim. – Sapa