Although no date has been set for such a vote, Chief Justice Mogoeng Mogoeng said the National Assembly speaker had the authority to order a secret ballot in a case brought by the country's opposition parties.
"The speaker of the National Assembly has the constitutional power to prescribe that voting in a motion of no-confidence in the President of the Republic of South Africa be conducted by secret ballot," the chief justice said.
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Opposition parties have lobbied for a secret ballot and called for African National Congress (ANC) lawmakers to "vote with their conscience", but Speaker Baleka Mbete had in April said she had no powers to approve a secret ballot.
"Whether the proceedings are to be by secret ballot is a power that rests firmly in the hands of the speaker, but exercisable subject to crucial factors that are appropriately seasoned with consideration of rationality," said Mogoeng.
The ANC holds a large majority in parliament and Zuma has survived similar votes in the past, which have not been secret.
Zuma's sacking of respected finance minister Pravin Gordhan in March fuelled public anger over years of government corruption scandals, record unemployment and slowing economic growth.
The president has recently faced unprecedented criticism from senior ANC figures, including Deputy President Cyril Ramaphosa.
Zuma, who came to office in 2009, is due to step down as head of the ANC in December, and as national president ahead of the 2019 general election.
He is seen as favouring his ex-wife, former African Union chief Nkosazana Dlamini-Zuma, to succeed him -- rather than Ramaphosa.