Mr Mbeki has come under fierce international criticism from mainstream scientists and medical experts for his unorthodox views and lack of government action.
But he said the government's response to the crisis assumed there was a link between the two.
His comments came the day after the Anglican Church in South Africa strongly criticised his government for refusing to provide medication for people with HIV.
In South Africa, 1,500 people are infected with HIV every day.
Mr Mbeki told hostile questioners in parliament: "The programme of the government in this country is based on this thesis that HIV causes Aids and everything in the programme says that."
Public anger
But he went on to say that that while the Human Immunodeficiency Virus (HIV) could be a contributory factor in causing Aids, it could not actually cause the syndrome.
Noting that Aids stands for Acquired Immune Deficiency Syndrome, he said: "A virus cannot cause a syndrome. A virus can cause a disease, and Aids is not a disease, it is a syndrome."
The president said questions about HIV and Aids had been raised by "very eminent scientists", and declared that while he could accept that HIV contributed to the collapse of the immune system, other factors like poverty and poor nutrition were also involved.
Mbeki isolated
There is growing anger in South Africa that so much time is being spent arguing over the issue, rather than treating people.
President Mbeki has found himself increasingly isolated over the past few days as members of his cabinet and government supporters have stated that they believe beyond doubt in the link between HIV and Aids.
Mr Mbeki has come under fierce international criticism from mainstream scientists and medical experts for his unorthodox views and lack of government action.
4.2m South Africans - about 10% of the population - were infected with HIV at the end of 1999, according to government figures,
The government refuses to supply the anti-retroviral drugs AZT or Nevirapine to pregnant women to prevent mother-to-child transmission, even though 5,000 HIV-positive babies are born every month.
Mr Mbeki said tests of Nevirapine were continuing in South Africa.
An advisory panel set up to research the link between HIV and Aids - which includes scientists who doubt the existence of Aids - would report back by the end of the year, he said.
"The basic problem is that many people don't want to study these questions," said Mr Mbeki. "They are perfectly happy to repeat what is said to be the conventional wisdom."