There are only two candidates in the hotly-contested race: Deputy President Cyril Ramaphosa, a wealthy businessman, and former minister Nkosazana Dlamini-Zuma, who is President Jacob Zuma's ex-wife.
Whoever wins will be well-placed to be South Africa's next president in the 2019 general election.
Voting started soon after midnight on Sunday and continued for nearly 12 hours after repeated delays due to disputes over which delegates were qualified to vote. Hundreds of attendees were banned from the poll creating the risk of legal disputes.
Allegations swirled of delegates being targeted with bribes, but ANC spokesman Khusela Sangoni told reporters that the process had proceeded "smoothly".
On Sunday, rival supporters sang and chanted in the conference hall outside Johannesburg as the vote was repeatedly postponed as arguments raged over delegates' credentials.
"I have not slept for the past 24 hours, but I don't care," said Patience Nomodi, 62, a party member for 40 years, wearing an ANC blanket on her shoulders and supported by a yellow walking stick.
In the early hours of Monday, fatigued delegates wearing the ANC's official colours of yellow and green napped around the conference centre, while others prayed exuberantly for their chosen candidates.
Ramaphosa-supporting delegate Siya Kolase told AFP after voting early Monday that he was confident his candidate would emerge victorious.
"He will address the issue of corruption. He is going to stabilise our economy," Kolase said.
The ANC, which has ruled since 1994 when Nelson Mandela won the first multi-racial vote, could struggle to retain its grip on power in the 2019 election due to falling public support.
"I'm bowing out very happy because I think... I made my contribution, so I'm very happy," said Zuma Monday as he walked around the vast tightly-secured Nasrec conference centre that is hosting the conference.
In his farewell address, Zuma appealed for unity in a party riven by bitter factions, and blamed the decline in the ANC's popularity on "perceptions in society that we are soft on corruption, self-serving and arrogant".
Senior ANC officials are divided between Dlamini-Zuma and Ramaphosa, and analysts say the leadership battle could end up splitting the party.
The ANC is still South Africa's biggest party by far, but the 54 percent it won in local elections last year was its worst poll result since 1994.
In opposition, the Democratic Alliance and the Economic Freedom Fighters are hoping to exploit the ANC's woes in the 2019 election, with one possible outcome being a coalition government.
Soaring unemployment and state corruption have fuelled frustration at the ANC among millions of poor black South Africans who face dire housing, inadequate education and continuing racial inequality.
Her critics have warned she will pursue Zuma's failing economic and political policies.
The couple had four children together before divorcing in 1998.
Ramaphosa, 65, a former trade union leader, led the historic negotiations in the 1990s to end apartheid before launching a business career that made him one of the country's wealthiest men.
He is often accused of failing to confront Zuma while serving as his deputy since 2014.
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