Mbeki, who has been mediating the Zimbabwe matter since 2007, is pushing for talks that would pave the way for a power-sharing deal between President Robert Mugabe's ruling ZANU-PF and Morgan Tsvangirai's Movement for Democratic Change.
The South African leader has resisted Western calls to condemn Mugabe for holding a presidential election marred by violence and boycotted by Tsvangirai.
African leaders at a summit in Egypt issued a resolution calling for Mugabe's government and the MDC to negotiate a unity government, with Mbeki continuing in his role as mediator.
"The AU and SADC (Southern African Development Community) cannot dictate the outcome of negotiations between Zimbabwe and political parties," Mbeki told the South African Broadcasting Corp.
He also bristled at an EU declaration, made at the end of the African summit, that it would only accept a government led by Tsvangirai.
Neither side in the Zimbabwe crisis appeared ready to follow the line suggested by the AU.
Mugabe's spokesman rejected a Kenya-style power-sharing government and the MDC ruled out negotiations.
MDC Secretary-General Tendai Biti said on Tuesday that Mugabe's decision to go ahead with the June 27 election "totally and completely exterminated any prospects of a negotiated settlement".
AU SPLIT ON MUGABE
Mugabe, 84, was sworn in for a new five-year term on Sunday after election authorities announced he had won about 85 percent of the vote in the run-off, which was condemned by monitors and much of world opinion as violent and unfair.
Tsvangirai defeated Mugabe in the presidential vote on March 29 but failed to win an absolute majority.
The MDC leader reluctantly agreed to participate in the run-off but pulled out less than a week before because of violence in which he said nearly 90 of his followers were killed. He was arrested five times during the campaign.
There are fears Zimbabwe may be engulfed by further violence if the MDC and trade unions take to the streets to protest Mugabe's election rather than negotiate with the Zimbabwean leader, who has ruled since independence from Britain in 1980.
Although there is support for a power-sharing deal modelled on the one that ended post-election violence in Kenya earlier this year, the AU is split on how to deal with Mugabe, still seen by many in Africa as a hero of the anti-colonial struggle.
In the strongest public statement from one of Zimbabwe's neighbours since Mugabe's victory, Botswana called for Mugabe to be barred from the AU and SADC. Kenyan Prime Minister Raila Odinga also has called for Mugabe to be suspended from the AU.
The summit did not back a U.S. push for U.N. sanctions against Mugabe, including an arms embargo.
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