The effort has been broadly welcomed on the continent, but at a joint news conference, some well-known differences between the U.S. and South African leaders were evident.
Most African leaders have expressed gratitude for President Bush's $15 billion pledge to fight AIDS, which has now infected an estimated 30 million people across the continent. The five year plan is intended to prevent seven million new infections, treat two million infected people and help care for 10 million AIDS orphans.
But here in South Africa, where the government has resisted pressure to provide anti-retroviral drugs, Mr. Bush's emphasis on treatment threatens to become a point of contention between the two nations.
President Mbeki has previously expressed doubt about the link between HIV and AIDS and the usefulness of anti-retroviral drugs.
On Wednesday, Mr. Mbeki avoided specifics, but said the United States had asked South Africa to come up with proposals for spending the new AIDS money. Although he mentioned treatment, he did not specifically mention the drugs.
And in the past, Mr. Mbeki has emphasized the importance of improving nutrition and easing poverty as ways to fight AIDS, rather than drugs.
President Mbeki said, "The U.S. government is taking a comprehensive approach to this which would therefore include questions of awareness, questions of health infrastructure, questions of treatment and so on, so we will look at the totality of those in the proposal that we would make."
President Bush, however, clearly sees providing anti-retroviral drugs as the continent's most urgent AIDS need.
President Bush said,"We need a common-sense strategy to make sure that the money is well spent. And the definition of well-spent means lives are saved, it means good treatment programs, good prevention programs, good programs to develop health infrastructures in remote parts of different countries so that we can actually get anti-retroviral drugs to those who need help."
The president said Africans have the will to fight AIDS, but often not the resources. He said the United States is willing to provide those resources. He also praised South Africa for recently increasing its anti-AIDS budget.
Protesters in South Africa have been pressuring the government to start making anti-retroviral drugs available to the country's estimated five million infected people. Neighboring Botswana, which has the highest HIV infection rate in the world, started an anti-retroviral program last year.
But the South African government has so far resisted that pressure, arguing that such a program is not financially feasible. Many observers, however, believe that the resistance is more ideological than fiscal.
They point, for example, to a recent attempt by the South African government to block treatment money granted by the United Nation's Global Fund to Fight AIDS to a program in the Kwa Zulu Natal province.
The government initially said that money should go into the national anti-AIDS budget, but it now says an agreement has been reached. South Africa's cabinet is now investigating the possibility of a treatment program, but the expected announcement has been delayed for more than a month.
Questions also remain in Africa about whether the United States will fully fund Mr Bush's AIDS emergency plan. The president asked Congress for only $1.7 billion of the $3 billion that had been expected in the program's first year.