After a rocky start to the gathering, two candidates accepted the party's nomination for president: Nkosazana Dlamini-Zuma, former African Union commission chair and Zuma's ex-wife, and Deputy President Cyril Ramaphosa, a wealthy businessman who has been increasingly critical of the president.
Ramaphosa is the 14th president of the ANC after 2 440 delegates voted for him to lead the country's governing party for the next five years.
Mr Ramaphosa was widely considered the sensible choice in the election.
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Ramaphosa's support base during his presidential campaign was derived from a strong anti-Zuma movement within the ANC, from various unions including Cosatu, and also from within the business sector.
In a boost to Ramaphosa, courts ruled that officials from some provinces seen as supporting Dlamini-Zuma had been elected illegally and were barred from the conference.
"If Ramaphosa does not recall Zuma, his hands will essentially be tied behind his back and Zuma will have one court case after another so as to keep plundering state assets and ensure that all the rotten-apple ministers are retained", Groenewald said.
Despite being part of Zuma's administration, the 65-year-old Mr Ramaphosa has promoted himself recently as a reformer who will steer South Africa away from the scandals that have bedevilled the ANC.
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He was also viewed as an anti-corruption candidate, with his opponent expected to protect her former husband against 783 allegations of corruption.
The vote was a long and acrimonious process.
"I hope you will cooperate with the new leadership.as we move to the 2019 elections", Baleka Mbete, party chairwoman, asked hopefully of delegates.
There were jubilant scenes at the ANC conference after it was announced Ramaphosa (left) had won.
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