He was the only candidate nominated by parliament, which is dominated by his African National Congress. MPs broke into song at the announcement.
In his first presidential speech, Mr Ramaphosa, 65, said he would tackle the corruption which allegedly became widespread under Mr Zuma.
The ANC had told Mr Zuma to step down or face a vote of no-confidence.
Mr Zuma faces numerous corruption allegations but denies any wrongdoing.
One allegation is that he allowed the wealthy Gupta family, who whom he has personal ties, to wield influence over policy, in an example of "state capture".
An arrest warrant has been issued for Ajay Gupta, one of the three most prominent Gupta brothers, officials said on Thursday.
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