Mr Zuma trounced deputy president Kgalema Motlanthe, his only challenger who ran a largely muted and reluctant campaign, getting 2,983 votes to 991.
The ANC voted to install wealthy businessman Cyril Ramaphosa as deputy president of the party, sending Mr Motlanthe out of the top rungs of power after his challenge.
Around 4,000 delegates voted in the ANC's leadership contest at the party's Mangaung conference, being held in the city also known as Bloemfontein.
The run-up to the conference saw disrupted provincial meetings, threats and shootings of local ANC officials, as corruption allegations trailed from the smallest local government to Mr Zuma at the top. That had many wondering whether the ANC still remains the party of reconciliation and racial fellowship that Nelson Mandela and others envisioned.
Mr Zuma, 70, was the favourite heading into the conference after winning the nominations in most provincial ANC polls. He has wide support among Zulus, South Africa's largest ethnic group, as well as from a loyal cadre of government and party officials.
But many in the public have grown disenchanted with Mr Zuma, who former president Thabo Mbeki fired as deputy president in 2005 after he was implicated in the corruption trial of close friend and financial adviser Schabir Shaik over a 1999 arms deal. Newspapers have written numerous articles recently about the millions of dollars of government-paid improvements made to Mr Zuma's private homestead. Mr Zuma has also faced accusations, by the media, of being unable to manage his personal finances and relying on friends and colleagues to bail him out.
Mr Zuma has faced criticism over his sexual activity. He was put on trial on charges of raping a family friend, and acquitted, in 2006. He also outraged Aids activists by saying that he had unprotected, consensual sex with the HIV-positive woman and then took a shower in the belief that it would protect him.
He and the ANC have also been criticised for strikes that overtook the nation, particularly in the mining sector, and the handling of violence at the Lonmin platinum mine in Marikana in August that saw more than 46 people killed and sparked violence and labour unrest at other mines.