"President Zuma extends his congratulations and best wishes to President Kenyatta and the people of the Republic of Kenya," said a statement from the Department of International Relations.
It added: "South Africa and Kenya share a long historical relationship and President Zuma said South Africa looks forward to working with Kenya under President Kenyatta to consolidate relations and implement existing agreements."
Kenyatta was declared the winnerof a disputed poll on Friday, beating his long-time rival Raila Odinga by a huge margin.
The east African nation's election commission said Kenyatta won Tuesday's election with 54% of the vote.
The commission labelled the vote as "credible, fair and peaceful".
Following the announcement of results, hundreds of police in anti-riot gear were in the streets of the capital, Nairobi, amid fears of further protests by opposition supporters.
The opposition called the vote a "charade" and said that going to court to challenge it was not an option.