After mediating three days of talks between the rivals in the Zimbabwean capital, Mbeki said he knew of no deal being signed, adding that he remained confident all three sides could find an agreement.
"We have dealt with all the elements on which president Mugabe and Mutambara agree, but there is disagreement on one element over which Morgan Tsvangirai had asked for time to reflect," Mbeki said.
"We have adjourned to give Morgan Tsvangirai more time to consider these matters.
"I'm quite confident they will resolve all their outstanding matters which would result in this inclusive government and, in the second instance, then acting together," Mbeki told reporters.
Welshman Ncube, secretary general for Mutambara's faction, emphasised that "no deal has been signed by anyone. Dialogue is still continuing".
Mbeki met Angolan president Jose Eduardo dos Santos on Wednesday in Luanda, Angolan state radio reported, and was expected to return to South Africa afterwards ahead of a summit of regional leaders this weekend.
He was to give a report to the Southern African Development Community (SADC), Mukoni Ratshitanga, a spokesman for Mbeki, said, adding: "After that we are going back home."
Mbeki has been appointed mediator for the Zimbabwe crisis by SADC, a 14-nation regional bloc, and had arrived in Harare over the weekend for negotiations between Mugabe, Tsvangirai and Mutambara.
"The talks are adjourned, not ended, but I wouldn't say until when. Tsvangirai needs more time to consult," Mbeki's spokesman told the AFP news agency.
Asked earlier whether signatures had been put to a deal, Mbeki said, "I wouldn't know about it. We are facilitating discussions among three parties."
Negotiations have reportedly included proposals for Mugabe, who has ruled since independence from Britain in 1980, to take on a more ceremonial role in exchange for amnesty from prosecution, with Tsvangirai being made executive prime minister.