The High Court in Johannesburg on Friday set aside the suspension of Cosatu general secretary Zwelinzima Vavi.

"The decision... is declared invalid... and accordingly set aside," Judge Phineas Mojapelo said.

The judge said the Congress of SA Trade Unions central executive committee (CEC) had the right to suspend Vavi, but found that it had failed to comply with the trade union federation's constitution.

"They did not vote when a vote was prescribed. No valid decision was taken in those circumstances," Mojapelo said.

He ordered that Cosatu pay the costs.

In August last year, Cosatu said Vavi had been put on special leave pending the outcome of a disciplinary hearing relating to his affair with a junior employee.

In July, the employee accused him of rape. He said they had an affair. The woman subsequently withdrew a sexual harassment complaint against him.

Following Vavi's suspension the National Union of Metalworkers of SA (Numsa), an ally of his, lodged an application in the High Court in Johannesburg challenging the decision.

Vavi then lodged papers to be added as an applicant in Numsa's challenge.

In these, he asked the court to grant him an interim order interdicting and restraining Cosatu from enforcing any decision taken at its CEC meeting in August.

Courtroom 11C erupted into cheers from Numsa members and Vavi supporters when Mojapelo concluded his judgment.

Vavi's wife Noluthando was in court along with Numsa deputy general secretary Karl Cloete. Vavi was not in court because his daughter was in a car accident in Queenstown, Eastern Cape on Thursday.

Speaking outside the court, Noluthando told reporters she felt justice had been done.

She thanked those who had fought for her husband but also questioned why Cosatu had treated Vavi in this way.

"Why persecute your own... What has my husband done? I'm feeling so sad."

Noluthando said she was relieved that the court had ruled in Vavi's favour and wanted to see him back at Cosatu.

Cloete, also speaking outside court, said Numsa welcomed the judgment.

"[The judgment] has vindicated our long-standing belief that the suspension was politically engineered to undo the democratic choice of worker delegates... Who in September 2012 democratically elected comrade Vavi," he said.

"While we are relieved that this costly but avoidable court battle is over, we hope the Cosatu leadership will have the political and organisational discipline to respect the decision of the court and abide by it fully."

Cosatu is holding a special CEC meeting in Johannesburg on Tuesday where the judgment will be discussed as well as a way forward.

Spokesman Patrick Craven said the court's decision was noted and respected.

Numsa and nine other affiliates are calling for Cosatu to hold a special congress where new leadership will be elected. Cosatu, however, has said no to a special congress.

Numsa spokesman Castro Ngobese said the union had sent a letter to Cosatu giving its president Sidumo Dlamini 48 hours to announce a special congress, otherwise the metalworkers union would take the matter to court.