Mr Zuma trounced deputy president Kgalema Motlanthe – his only challenger who ran a largely muted and reluctant campaign – getting 2983 votes to 991.
The ANC voted to install wealthy businessman Cyril Ramaphosa as deputy president, sending Mr Motlanthe out of the top rungs of power after his challenge.
Around 4000 delegates voted in the leadership contest at the ANC's Mangaung conference.
The run-up to the event 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 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 also faced criticism over his sexual activity and was put on trial on charges of raping a family friend in 2006, but was acquitted.
He and the ANC have also been criticised for strikes in the mining sector, and the handling of violence at the Lonmin platinum mine in Marikana in August.