The First National Bank (FNB) said the measure was the result of legal action taken by the liquidators of another bank, which is owed money by the 81-year-old politician.
"FNB was instructed by the High Court to place a hold on outgoing payments from former President Zuma's FNB accounts. The accounts are not closed as incoming payments are unaffected," FNB told AFP.
"This instruction from the court results from the process currently being managed by the VBS Bank liquidators, and FNB was legally required to comply. Former President Zuma's recourse now lies with the courts and VBS liquidators."
The measure is likely to further taint the reputation of graft-accused Zuma ahead of general elections on May 29.
In power from 2009 to 2018, Zuma is fronting a small start-up party that is threatening to take away key votes from his old home, the African National Congress (ANC).
The partial account freeze is related to the decade-old, controversial renovation of Zuma's massive homestead in his home province of KwaZulu-Natal.
In 2016 a top court found that the then-president had acted against the constitution by using millions of dollars of state funds to refurbish his rural Nkandla home in the name of "security upgrades."
Some of the features included a chicken coop and a swimming pool, alleged to be a fire-fighting facility — coined 'fire pool'— a cattle enclosure and an amphitheater.
Ordered to pay back the money, Zuma took out a 7.8 million rand ($413,000) loan from VBS.
The bank was later placed under curatorship, and its liquidators have gone to court to force Zuma to pay back the outstanding part of the loan.
Partial Freeze Ordered on Bank Account of Former South African President
JOHANNESBURG—A South African bank said on Wednesday a court had ordered a halt to outgoing payments from ex-president Jacob Zuma's accounts in a dispute over loans for improvements to his private home while in power.
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