A packed Midrand conference venue broke out in song as Zuma, who had been waiting for President Thabo Mbeki to finish his address, walked into the auditorium.
The crowd, estimated to be more than 3000, sang struggle songs to welcome Zuma at the congress.
Zuma arrived an hour after Mbeki.
He waited for a few minutes at the door leading into the conference venue so that he would not disturb Mbeki who was addressing the delegates.
As Zuma made his way to the stage where Mbeki was seated, certain Cosatu members ululated and cheered in support of the deputy president.
Cosatu general secretary Zwelinzima Vavi said corruption allegations against Zuma were serious, but Cosatu was of the view that the labour federation should support him.
"Cosatu will continue to hold the view that the deputy president remains a leader we respect, admire, for his utmost service to the people.
"To that end, he remains innocent until proven guilty," said Vavi to a rapturous applause.
Zuma, who would not be prosecuted after corruption allegations against him emerged in the arms deal, was accused of trying to solicit a R500 000 bribe from a French arms manufacturer that benefited from the deal.
Vavi said the allegations against Zuma should not be allowed to continue as they would further tarnish the image of the deputy president, and undermine public confidence in democratic institutions.
He said: "It would be a blow to working people if the investigations drag on or, worse, support the allegations.
"The spectacle of mudslinging, character assassination and leaks to the media has become extraordinarily destructive.
"It now represents the biggest threat to our movement, undermining unity, confidence and coherence. "We need decisive leadership on this issue. We can tolerate neither a cover-up of corruption nor the unfair crucifixion of our leaders in the press.
"We simply cannot afford to let this issue drag on," Vavi said.
"The deputy president has played a critical role in the alliance, and the campaign on HIV/Aids".
Zuma, who was not scheduled to speak at the congress, urged delegates to defend South Africa and freedom against people he termed counter-revolutionaries.
"It is our duty... to deepen democracy in South Africa and defend the country against fly-by-night counter-revolutionaries because no one will do that on our behalf.
Delegates denounced, in song, National Prosecution Authority head Bulelani Ngcuka for investigating Zuma "Ngcuka uvulela impi, ubiza umlo. (Ngcuka you are calling for war)," sang a group outside the entrance of the congress venue.
"Wena ulawula ama Scorpions sitshele ukuthi uZuma wethu wenzeni? (Head of the Scorpions tell us what our leader has done?)" – Sapa.
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