Mbeki was due to stand down next year after two terms in office, but faced growing pressure from supporters of ANC President Jacob Zuma to quit following a judge's ruling that he was instrumental in Zuma being charged with corruption.
African National Congress secretary-general Gwede Mantashe said Saturday that the party's top-level National Executive Committee has "decided to recall the president of the republic before his term of office expires."
"(Mbeki) did not display shock ... He welcomed the news and agreed that he is going to participate in the process and the formalities," Mantashe said.
Mantashe said that Mbeki would remain in the top office until an interim president was appointed and would continue as mediator in Zimbabwe, where last week he persuaded President Robert Mugabe to cede some power to the opposition for the first time in 28 years.
Mbeki, who succeeded Nelson Mandela in 1999, has been heralded by the international business community. If other key cabinet ministers decide to quit in solidarity, there could be turmoil.
Several key government executives, including Deputy President Phumzile Mlambo-Ngcuka, already have indicated they will do so.
All eyes are on Finance Minister Trevor Manuel, who shares the credit with Mbeki for South Africa's sustained economic growth and investor-friendly policies over the past 10 years.
Mantashe said Zuma was meeting with Cabinet ministers to persuade them to remain in government. He said there was no decision on whether to hold early elections and that parliament would meet in the near future to formalize Mbeki's resignation.
He said top priority at the moment was to focus on "ensuring the smooth running of the country."
"We share the desire for stability and for a peaceful and prosperous South Africa," he told a news conference.
Mbeki fired Zuma as his national deputy president in 2005, after Zuma's financial adviser was convicted of trying to elicit a bribe to deflect investigations into a multibillion-dollar international arms deal.
The charges were withdrawn against Zuma, but the chief prosecutor announced in December he had enough evidence to bring new ones. This was within days of Zuma ousting Mbeki as ANC president.
In a ruling last Friday that threw out corruption charges against Zuma, Judge Christopher Nicholson said it appeared Mbeki and his justice minister had colluded with prosecutors against Zuma as part of the "titanic power struggle" within the ANC.
Mbeki indignantly denied this Friday.
"It impoverishes our society that some resort to the tactic of advancing allegations with no fact to support these," the presidency said in a statement. "The question will have to be answered now what kind of society are we building, informed by what value system and with what long-term effect to the political and overall moral health of the nation?"
By Associated Press Writer Donna Bryson