After nearly two hours of speeches, members of parliament voted in the secret ballot on the floor of the South African Parliament.
President Jacob Zuma faces a no-confidence vote in the country's parliament.
Opposition parties believe that MPs from the governing African National Congress (ANC) would be more likely to vote against the president if their vote is secret.
Zuma's term as South Africa's president is due to run until 2019.
A 201-vote majority would be needed to remove him from power, and the ANC holds 249 seats in the 400-seat parliament.
"The reason that it was decided‚ the Speaker decided‚ that they should have the responsibility to vote secretly‚ is so that they should vote truthfully‚ without fear that maybe the party‚ in this case the ANC‚ might banish them if they vote in support of the motion of no confidence..."
The head of the main opposition Democratic Alliance party, Mmusi Maimane, is urging lawmakers to "take our country back".
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Zuma, who has held power since 2009, has now survived nine no-confidence votes despite a record in office marred by allegations of sleaze and influence-peddling.
If the ruling African National Congress party, which has the clear majority in parliament, can not agree on a candidate in that time, new national elections would be held.
The African National Congress on Wednesday said the Democratic Alliance's plans to bring a motion calling for early national elections showed that it did not respect the will of the people and was intent on "regime change".
South Africa's rand weakened almost 1.5 percent immediately after the news of Zuma's victory, with markets perceiving his survival as a negative.
The opposition party leader added that Zuma was the embodiment of "what the ANC has become - a toxic mix of corruption, cronyism and nepotism", and that he was a norm within the party, rather than an exception. After a chorus of shouts responded to each call for votes in favor and against, she pronounced, "I think the "no's" have it". "The people of South Africa also look to parliament for signals of hope", said Mbete, a longtime Zuma ally.
Demonstrations both for and against Zuma are planned in front of the parliament building before the much-anticipated vote.
"Mbete's decision was made knowing that Zuma will be secure", Darias Jonker, of the New York-based Eurasia political analysis consultancy, said.