Hogan was kept on by Zuma, but reassigned to the public enterprises portfolio, and Aaron Motsoaledi, a provincial education minister and medical doctor took over as health minister, inheriting a struggling health system and an ever-growing HIV epidemic.
About one in every six South Africans, 7.5 million people, is HIV positive, with an estimated 750,000 now receiving antiretroviral treatment.
Several theories are circulating as to why Hogan may have been moved out of the position. Earlier this year, she publicly criticized the African National Congress (ANC) for barring the Dalai Lama from a conference on peace and reconciliation. But more likely the cause for the change, according to South African news reports, is that Hogan may have questioned ANC plans for a publicly funded national health insurance initiative.
Thabo Masebe, a presidential spokesperson denied that there was any reason for Hogan's replacement other than Zuma's decision that Motsoaledi was better suited for the job.
"When he appoints people to serve in the cabinet that is not a statement of 'No confidence' in people that held the position before," said Masebe.
"He looked at the team and found that Motsoaledi is the person who fits the profile of what he wanted."
Zuma himself has caused concern among HIV advocates in the past. In 2006, he revealed that after knowingly having sex with an HIV-positive woman, he showered because he thought it would reduce his risk of infection.
Though Hogan is not a doctor and had limited health experience when she became health minister, she had the support of many advocates because of her strong and public stance against former President Thabo Mbeki's denial that HIV causes AIDS and his administration's slow movement to address or even acknowledge the problem.
Mbeki's health minister, Manto Tshabalala-Msimang, became infamous for her recommended herbal remedies for AIDS, and even after the government announced in 2003 that it would provide antiretroviral treatment to HIV-positive South Africans, many HIV-positive people remained without treatment.
Rebecca Hodes, director of policy, communication and research for the Treatment Action Campaign, or TAC, a group that was instrumental in getting the government to agree to provide treatment, said the group is disappointed about Hogan's replacement.
"[Hogan] supported TAC at a time when very few people were coming out against President Mbeki's AIDS' denialism," said Hodes. "She was one of the most outspoken critics."
When Hogan took over for Tshabalala-Msimang in September of 2008, one of the first things she did was tell the public that HIV causes AIDS.
For those working in the public health field it was a much-needed change.
"She set a different tone on HIV, she said it was a crisis--was unambiguous about the need to ensure people get access to treatment," said Mark Heywood, deputy chairperson of the South African National AIDS Council, a group set up by the government to advise on issues regarding HIV/AIDS research treatment and prevention.
"The council was very satisfied with Barbara Hogan as minister of health," he said.
Motsoaledi meanwhile, has had a relatively low profile, and while he has been in charge of health affairs in the province of Limpopo in the past, his views on HIV/AIDS policy are not widely known. Few in the public health field seem ready to pass judgment on the new minister, but there is some concern.
"Certainly I would say we are nervous about this appointment, it could turn out to be a very good one, but it's an unknown quantity to many of us in the field," said Heywood.
Hodes said she isn't quite sure what to expect from the new minister but that he has many challenges ahead of him, especially with the growing number of HIV-positive people dying of tuberculosis, now the leading cause of death in South Africa.
One of the most important tasks he will have, said Hodes, is to ensure that the poorest sectors of South African society do not suffer disproportionately from the fall-out of the global economic crisis.
"We just have to wait and see. We are welcoming him with reservation," she said. "He has a massive pandemic to confront."