The final vote was 198 to 177, with nine abstentions.
Opposition parties have lobbied for months for an anonymous no-confidence vote to provide cover to disgruntled members of Zuma's African National Congress who may fear coming out against their leader in an open ballot.
Ramaphosa is viewed as more investor friendly and has pledged to fight the corruption that has plagued Zuma's tenure. 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.
Zuma's critics see him as having delegitimized the ANC, the liberation movement that has governed South Africa since the election of Nelson Mandela.
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Baleka Mbete, the country's parliament speaker, made the decision to hold the vote in secret on Monday after opposition parties took the case to the Constitutional Court. "The choice before us is a simple one".
"We have got to get rid of this man before he destroys everything that we have all worked so hard for", said another protester, Anne Shirley.
"It has been the publicly stated intention of the opposition... to sow seeds of chaos in society to ultimately grab power", it said in a statement.
A court a year ago found him guilty of violating the constitution after he refused to repay taxpayers' money used to refurbish his private rural house.
Urging the ANC to fire Zuma, she said it was not a motion to remove the ANC or the ANC-led government, but a move to remove Zuma. He has been under fire for numerous allegations of corruption. And despite street protests, opposition maneuvering, and defections from his own party, he has always refused to step down voluntarily. This will be the eighth such vote in Zuma's tenor as president, although this time there is a clear factional divide within the ruling African National Congress (ANC).
Zuma's replacement is set to be chosen at a party conference in December this year.
The result suggests that at least 26 of the ruling party's 249 members voted with the opposition, who had taken pains to portray their motion as an attempt to dislodge a weak and unpopular president, not an assault on the ANC.