Zuma's supporters have been demanding that votes be counted by hand instead of using electronic means; their argument that the process must be transparent insinuating that the Mbeki era has not been transparent.
More than 4,000 delegates are to determine the outcome of the leadership election in a secret ballot.
If Zuma wins, he will almost certainly also succeed Mbeki as the country's president in 2009 due to the party's electoral dominance.
Mbeki is barred by the country's constitution from seeking a third term as the country's 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, and Zuma supporters, who appeared to outnumber those of Mbeki inside the conference hall, demanded that Lekota be removed from his role as chairman of the conference on Sunday.
Lekota battled to be heard against Zuma supporters singing the anti-apartheid song Bring Me My Machine Gun, which has become Zuma's anthem.
Addressing the conference on Sunday, Mbeki called for unity and a restoration of the "moral force of our movement, urging delegates to choose an "ethical" leader.
"During the years since our liberation in 1994, certain negative and completely unacceptable tendencies have emerged within our movement, which threaten the very survival of the ANC as the trusted servant of the people it has been for 96 years," he said.
"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 has taken the lead in branch elections over Mbeki for the ANC presidency, winning 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 before the conference.
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, creating a very difficult situation.
The relationship between the two men has become strained, leading to a split in the party.
Zuma is a controversial figure. He was acquitted of rape last year but is still under investigation for corruption.
Mbeki fired Zuma as the country's deputy president in 2005 after Zuma's financial adviser was convicted of trying to elicit a $70,000 bribe for Zuma to deflect investigations into an arms deal.
Charges were withdrawn against Zuma but the National Prosecuting Authority has indicated it may revive them.
Zuma was also charged with raping a family friend but was last year acquitted.
Aids activists were outraged, however, when he testified that he had had unprotected, consensual sex with the HIV-positive woman and then took a shower in the belief that it would protect him from the AIDS virus.
He survived both those scandals, successfully portraying himself as a victim of a plot to stop him becoming president.
On Saturday, an affidavit containing what it calls substantial new evidence that Zuma received larger payments in the corruption case than originally thought was filed by South Africa's directorate of special operations.
"The extent and gravity of the charges has grown...," said the affidavit, which was a response to an appeal by Zuma.
Zuma has said that if elected as ANC president, he will not step down unless he is found guilty in court.
Much has been made of the personality and class differences between the two former allies, who are both 65 and spent years in exile during apartheid.
Mbeki, a foreign-educated academic who sprinkles his speeches with Shakespeare, is seen as aloof. He spearheaded the country's economic boom but has alienated the poor, who feel they have not benefited nearly 13 years after the end of apartheid.
Zuma, who had no formal schooling and was a leader of the exiled ANC's military wing, is much more populist and has strong backing from the union movement, which wants him to push through more pro-poor policies.
There are fears that Zuma could tilt the government sharply to the left and he has held talks with business leaders in South Africa and abroad to try to soothe investor concerns.
Despite the perceived differences, Adam Habib, a political analyst at the University of Johannesburg, said any change in policy under Zuma would be "in line with what has been happening over the last three or four years".
"I don't think there would be a fundamental change of policy, if either were elected," he said.
Meanwhile, two of South Africa's most powerful moral voices have spoken out on the matter.
Nelson Mandela, the 89-year-old former president, who has retired from politics but who is still seen as a unifying figure in the country, expressed his concern at the divisions in the party.
"It saddens us to see and hear of the nature of the differences currently in the organisation," he said in a message to the delegates distributed by the South Africa Broadcasting Corporation.
"Whatever decision you are to make at this conference, including decisions about leadership positions in the organisation, let the noble history of the ANC guide you."
On Friday, Archbishop Desmond Tutu, one of the country's most powerful moral voices, urged the ANC not to elect Zuma, someone whom he came out against following the rape charge.
Tutu pleaded with delegates to "not choose someone of whom most of us would be ashamed".