He has now survived nine no-confidence votes, one for each year that he has been in office, which is due to run until 2019 when national elections are expected.
While Members of Parliament (MPs) used their allocated time in Parliament to have their say, the crowds outside waited anxiously for the result of the vote.
South Africa's main opposition party is accusing President Jacob Zuma of "derelict leadership" in its draft resolution in parliament asking for his removal from office.
The delay in hearing the debate was partially attributed to a Constitutional Court application moved by opposition parties, UDM (United Democratic Movement) and EFF (Economic Freedom Fighters).
ANC stalwarts and veterans wrote an open letter on Sunday to MPs.
None of the ANC's defenders chose to explain why Zuma was a fit and proper person to continue as president of the country. We should not use other tactics to get rid of a governing party. Some party members quickly denounced those who voted against Zuma as sellouts, and chief whip Jackson Mthembu said the party would consider disciplining them.
Opposition to Zuma's rule, however, has been growing amid revelations of corruption and influence peddling, even as the economy has faltered and unemployment has remained stubbornly high in a country marked by deep inequalities of wealth.
No one is to disclose the results, in any way whatsoever, before the Speaker announces the results in the Assembly.
Zuma has previously weathered seven similar votes - but never any under the cover of secrecy. "Ours, today, is not against the ANC but against the father of Duduzane", Malema told the house. And that is why we are here to make it very clear that ours today is not against the ANC, but against the father of Duduzane.
Several opposition parties led thousands of anti-Zuma protesters outside parliament, while supporters of the president held a rival march.
"My conscience is that we need to respect the voters that brought us here", she said.
Parliamentary speaker Baleka Mbete chose to make the secret ballot after an opposition party moved the case to the Constitutional Court to enable more ANC members of parliament to break party ranks, CNN reported.
The parliament has 400 members with an outright majority of over 240 belonging to the ruling party. Opposition parties hope it will encourage disgruntled legislators with the ruling African National Congress party to vote against Zuma. "Our vote is a protest against corruption, maladministration and the thinning of public resources".
The ANC's alliance partners, the South African Communist Party and COSATU, a coalition of trade unions, told Zuma to quit.
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