Mbeki is barred by the country's constitution from seeking a third term as president. But if he were to remain the ANC leader, he would influence the party's choice for the next president.
Mosiuoa Lekota, South Africa's defence minister and a key supporter of Mbeki's bid for a third term as ANC leader, was heckled on Sunday when he called the party's leadership congress to order.
Lekota has repeatedly attacked Zuma, who has taken the lead in branch elections over Mbeki for the ANC presidency.
Zuma supporters have demanded that Lekota be removed from his role as chairman of the conference.
His supporters appeared to outnumber those of Mbeki inside the conference hall with Lekota battling to have himself heard against a chant in support of the 65-year-old who was sacked as deputy head of state in 2005 after his financial adviser was convicted of corruption.
Addressing the conference, Mbeki urged the delegates to choose a leader an "ethical" leader.
"The character of our movement at this juncture calls for a leadership seized with ethical fervour," he said during a three-hour speech defending his record.
Mbeki has been under fire for what critics say is an increasingly aloof and autocratic leadership style.
Zuma won the support of five out of the nine ANC provincial branches as well as the backing of the women's league and youth league in a first round of voting ahead of the conference.
A total of 4,075 delegates will determine the outcome of the leadership election in a secret ballot.
Al Jazeera's Mike Hanna in Polokwane said that a Zuma victory would mean that the presidency of South Africa and of the ANC would be held by different people for the first time in the party's 13 years in power.
"You would have a situation, if Jacob Zuma won, where the president of the country was separate to the president of the movement, and they are two people with very great personal differences as well," he said.
"It would create a very difficult situation indeed."
The relationship between the two men is fraught and has led to a split in the party.
Zuma is a controversial figure. He was acquitted of rape last year and could face fraud and corruption charges.
Documents containing new evidence against Zuma in a corruption case were filed by legal authorities on Saturday.
An affidavit was filed by South Africa's directorate of special operations.
It contains what it calls substantial new evidence that Zuma had received larger payments in a corruption case than originally thought.
"The extent and gravity of the charges has grown...," said the affidavit, which was a response to an appeal by Zuma.
Any charging of Zuma could lead to his jailing before being sworn in as ANC president.
Zuma said that he would not step down as ANC president if elected, unless he is found guilty in court.
There are fears that Zuma could tilt the government sharply to the left.
|"What we are likely to see is changes in policy that are in line with what has been happening over the last three or four years"|
Adam Habib, political analyst at the University of Johannesburg
However, Adam Habib, a political analyst at the University of Johannesburg, says that many of the cited differences between a Zuma and Mbeki leadership may not materialise.
"I don't think there would be a fundamental change of policy, if either were elected," he said.
"South Africa's macro-economic policy has already changed over the last three or four years. We no longer talk about privatisation. We have a state-led industrialisation drive. We have a huge number of people on social support grants."
"What we are likely to see is changes in policy that are in line with what has been happening over the last three or four years."
Were Zuma to win, Habib sees Mbeki as having to step down and ask the national legislature to choose a president from their own ranks or call early presidential elections.
If Mbeki wins, Habib says that power is likely to continue to be centralised but it will be contested more vigorously, as has happened recently with increasing opposition to Mbeki's consolidation of power in his national administration.