The Inkatha Freedom Party's Thembinkosi Francis Nxumalo won 54.99% support.
The ward was previously held by the ANC, whose candidate, Bongumenzi Mninimuzi Ngcobo, won just under 50% of the vote in the last municipal by-elections.
Nkandla has been in the news recently because this is where Zuma's private residence has recently been upgraded, at a reported cost of over R200-million.
Zuma, in Parliament recently, defended the costs associated with his Nkandla home. He said he was still paying a bank bond for the five family buildings that form part of the compound.
"My residence ... has been paid for by the Zuma family. All the buildings and every room we use ... was built by ourselves as family and not by government. I have never asked government to build a home for me, and it has not done so."
Zuma said violence in KwaZulu-Natal had led to his home being burnt down twice, and that he decided to extend the last rebuilt version while he was still deputy president.
"Then government came to say they now have to include the security features to my residence. By the time the government came the constructors were on site that had been enlisted by the family."
Zuma suggested investigators from the likes of the public protector's office should be "screened" before they are allowed to delve into his Nkandla residence because of its status as a national key point.
Zuma said he takes exception to accusations that government money was spent for his benefit.
"It is unfair, and I don't want to use harsher words because you believe that people like me can't build a home," he said, apparently referring to Democratic Alliance (DA) parliamentary leader Lindiwe Mazibuko, who had asked whether construction at the compound will be halted while the public protector investigates the spending.
The matter is currently being investigated by a public works task team.
The IFP also won Ward two, in Hlabisa, which was previously held by the National Freedom Party.
The councillor's post in the ward became vacant when the NFP's Mondli Jele resigned. Since last year's local government elections Hlabisa had been run by an ANC and NFP coalition.
The IFP retained ward 39 in KwaMashu, Durban, which was also contested by the NFP and the ANC.
The IFP and NFP have been at loggerheads in the ward since early August.
At least five IFP supporters or members and the son of an NFP leader have been killed in the area since then.
The ward was previously held by the IFP's Themba Xulu. He was found shot dead in Inanda on October 7 after being abducted from his home two days earlier.
The ANC managed to retain ward 72 of the eThekwini municipality.
The previous councillor Mthembeni Shezi, also known as Msizeni Ximba, was shot at while at a meeting at the Imbaliyethi High School on September 26.
Shezi, branch deputy chairperson Sbu Mpanza, and ward committee member Bulelani Mjoli were wounded in the incident. Shezi died in hospital the next day.
Ward three of the Msukaligwa (Ermelo) municipality in Mpumalanga, which was held by the ANC, was uncontested.
The ANC also retained ward 22 of the Lukhanji (Queenstown) municipality in the Eastern Cape and ward 12 of the Setsoto (Senekal) municipality in the Free State.
The Democratic Alliance retained ward two of the Bitou (Greater Plettenberg Bay) municipality in the Western Cape. – Sapa