The government and the opposition MDC are deadlocked over cabinet jobs and President Robert Mugabe has given key posts to his own Zanu-PF party.
Opposition leader Morgan Tsvangirai has threatened to pull out of the deal.
This is Mr Mbeki's first intervention since he stood down as president, just days after brokering the agreement.
The BBC's Jonah Fisher in Johannesburg says Mr Mbeki is effectively going to Zimbabwe as a private citizen, although he does have the backing of the regional group, SADC.
His policy of quiet diplomacy, which sealed last month's deal, may not hold much sway now that he has been forced to step down by his party, the African National Congress.
Our reporter says it will be interesting to see if Zimbabwe's veteran leader, 84-year-old Mr Mugabe, will be prepared to listen to him.
Local journalist Brian Hungwe in Harare says people in the capital hope Mr Mbeki's intervention will end the deadlock and their suffering.
'Jobs for the boys'
On Sunday, Mr Tsvangirai said that if Zanu-PF wanted the defence ministry, the MDC must have home affairs, which controls the police.
He told a rally in Harare: "If they [Zanu-PF] do it that way, we have no right to be part of such an arrangement.
"The people have suffered. But if it means suffering the more in order for them to get what is at stake, then so be it."
Zimbabwe's government says Mr Mugabe's actions do not violate the agreement.
A government list published on Saturday gave the main ministries, including defence, home, foreign affairs, and justice to Zanu-PF.
Zanu-PF believes the ministries allocated to the MDC are powerful, as they should be measured by their size of the budget.
For example, they argue since the education ministry gets a higher budget than home affairs or foreign affairs, it is a key ministry.
But MDC deputy leader Ms Thokozani Khupe sees it differently.
"It is about moving this country forward; it is about making sure the people of Zimbabwe have a better life, but for Zanu-PF it is jobs for the boys," she said.
Under the existing agreement, Mr Mugabe remains president while Mr Tsvangirai becomes prime minister.
Under the deal, Zanu-PF should have 14 ministries, Mr Tsvangirai's MDC 13 and a smaller MDC faction three.
As the impasse continues, Zimbabweans are having to deal with the continuing economic crisis.
"I think when Mbeki comes here he must settle this thing once and for all," one man in the capital told the BBC.
"Look at this nation, we are starving. The shops are empty. The whole township is stinking of rot, all the sewage is seeping in the houses."
New banknote
On Thursday, it was announced that Zimbabwe's annual inflation rate had soared to 231,000,000% - by far the highest in the world.
In August the government knocked 10 zeros off the currency, but this has failed to halt the rise of inflation and this week the central bank is issuing a new 50,000 Zimbabwe dollar banknote.
The UN says it needs $140m (£82m) for food aid in Zimbabwe over the next six months.
It says two million people are in need of food aid, and that the figure will rise to 5.1 million - or 45% of the population - by early 2009.
The current stalemate stems from disputed elections in March this year when Mr Tsvangirai gained more votes than Mr Mugabe, but not enough for outright victory.
Mr Tsvangirai then pulled out of a run-off vote in June, accusing Zanu-PF militia and the army of organising attacks on MDC supporters which left some 200 people dead.
Critics of Mr Mugabe say he triggered the economic crisis when he began seizing white-owned farms for land redistribution ahead of parliamentary elections in 2000.
But Mr Mugabe blames Western sanctions, which target him and his chief supporters, for wrecking Zimbabwe's economy.
BBC
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