Zuma won the backing of more than 75 percent of the ANC's 3,977 voting delegates at a party conference in Bloemfontein, making him the odds-on favourite to retain the presidency after 2014 general elections.
"The national conference has spoken and we are all part of that decision," a triumphant Zuma said in brief remarks to delegates.
Businessman Cyril Ramaphosa won the deputy presidency setting him up to become Zuma's eventual successor.
The vote took place despite the conference being threatened by right-wing extremists.
Police said four men plotted to kill country president Zuma, Motlanthe, government ministers and senior party officials. The men were charged with treason and terrorism.
Inside the conference there were also plots and intrigue.
Zuma had faced an embarrassing, if lacklustre, leadership challenge from Deputy President Kgalema Motlanthe, who won 991 of the votes.
The scale of Zuma's victory, dubbed a "Zumanami," prompted supporters to mock Motlanthe's camp, gesturing that their quest for change had gone "boom."
It will also take some of the heat off the embattled president.
"Zuma has not come forward with the fancy words, he has done his job. With this leadership we can go forward to 2014," said Tebogo Lekoloane, a voting delegate from Limpopo.
But after three years in power marked by crisis, Zuma faces a tough slog ahead.
He will have to work hard to win back South African voters, who increasingly see the ANC as out of touch, incompetent and corrupt.
Zuma's poll numbers have steadily eroded amid a series of scandals.
Criticism of his administration reached a crescendo earlier this year when police killed 34 striking miners in one day and it emerged that around $27 million (21 million euros) of taxpayers' money had been used to refurbish his private home.
A TNS South Africa poll released on Monday showed Motlanthe's approval ratings at 70 per cent, while Zuma polled 52 per cent -- less than the ANC's total at the last elections.
Despite public anger at the state of the country, the ANC is likely to romp home in 2014.
The ANC has consistently received around two thirds of the vote in previous elections since the end of apartheid.
But a poor showing could exacerbate divisions within Africa's oldest liberation movement.
With the opposition Democratic Alliance gaining traction in their personalised attacks on Zuma, the ANC could face a tough scrap to retain control of provinces like Gauteng -- which includes Johannesburg and Pretoria.
Zuma will also face an uphill struggle to correct the course of the ailing South African economy.
Unemployment remains stuck at around 25 percent and the economy is growing at its slowest rate in three years.
Meanwhile crucial sectors like mining have been hobbled by strikes over low wages and are struggling to modernise and reduce reliance on masses of cheap labour.
Credit ratings agencies have warned that further rating downgrades will come if the conference does not see the ANC change course.
Opening the five-day meeting Zuma tried to reassure investors that he does not back calls for mass nationalisations and that the country is not "falling apart."
The election of Ramaphosa as deputy head of the party -- putting him firmly in line to become deputy president -- may also assuage industry's fears.
"We are somewhat sceptical of the impact Ramaphosa can make though the market may interpret him, plus Zuma backing the National Development Plan as being a real positive," said Peter Attard Montalto, an analyst with Japanese bank Nomura.
"What we may have here then is a positive PR boost plus another investor-friendly voice in cabinet but little real change on the ground and in action."
For Motlanthe the outlook seems bleak.
He ran a largely silent campaign that has sometimes appeared more like a protest than a real run at the top office in the country. Defeat leaves him in the political wilderness, with uncertainty even he will remain as the country's deputy president.