Mbeki flew in from Johannesburg to join the ceremony and was met by Robert Mugabe, the Zimbabwean president, said Al Jazeera's Kalay Maistry from Johannesburg.
She added: "President [Robert] Mugabe has indeed met the leader of the opposition Morgan Tsvangirai. They were ushered into a room with South African president and the talks mediator Thabo Mbeki.
"So it is a very momentous occasion for Zimbabweans and everyone is hopig that this will now indeed be the first step in what will eventually lead to a lasting political and economic solution for zimbabwe."
International pressure for the parties to negotiate intensified after Mugabe won a one-man presidential run-off election, after it had been boycotted by Tsvangirai, the MDC leader, due to a wave of deadly attacks against his supporters.
The MDC says that at least 120 people have been killed in politically motivated violence.
Tsvangirai has previously refused to negotiate with Mugabe unless he and Zanu-PF recognised his victory in the first round of the presidential poll on March 29.
Memorandum of understanding
The South African government confirmed that Mbeki would fly to Harare, the capital, to oversee the signing between Zanu-PF and the MDC.
A foreign ministry statement read: "Mbeki will travel to Harare to facilitate the signing of a memorandum of understanding among the Zimbabwean political parties.
"The memorandum represents a positive step forward in the ongoing dialogue among the parties as facilitated by President Mbeki acting on behalf of SADC [Southern African Development Community]."
The move comes after a series of meetings between Mbeki, the rival parties and officials from the UN and African Union.
Haile Menkerios, the UN special representative to Zimbabwe, and Jean Ping, the African Union commission chairman, who met the parties over the weekend, had both expressed confidence the pact would be signed.
Menkerios said the draft, once signed, would clear the way for actual talks on the future of the country to take place.