Nozizwe Madlala-Routledge said she had been fired for going on an unauthorised trip to a Spanish Aids conference and for criticising hospital conditions.
She said it was her duty to respond quickly to reports that babies were dying in a maternity hospital.
Her sacking has been condemned by Aids activists and the opposition as a setback in the fight against HIV.
Some 5.5m South Africans are HIV-positive - more than in any other country.
In her first comments since her sacking, Ms Madlala-Routledge also said it was a known fact that there had been differences of opinion between her and Health Minister Manto Tshabalala-Msimang.
I acted in good faith in the belief that our president had approved the trip
The minister is known as Dr Beetroot after telling people with HIV to eat beetroot and garlic, while expressing doubts about the efficacy of anti-retroviral drugs.
Ms Madlala-Routledge said that she had criticised the minister's stance two years ago.
"She [Dr Tshabalala-Msimang] has said to me: 'I will fix you' and maybe she has fixed me," she told a news conference.
This has been denied by Dr Tshabalala-Msimang's office.
"No such statement was ever made," the department of health said.
BBC Southern Africa correspondent Peter Biles says Dr Tshabalala-Msimang is a close ally of the president.
Ms Madlala-Routledge denied local media reports that she had defied President Thabo Mbeki by going to Madrid with her son and a consultant, at a cost of 160,000 rand ($22,000).
"I acted in good faith in the belief that our president had approved the trip."
She said that in spite of her dismissal, she hoped to remain part of the campaign against HIV/Aids.
No official reason has been given for her sacking.