Nosiviwe Mapisa-Nqakula has been accused of abusing state resources for party political affairs.
The defense force had maintained that it was on an official mission and simply gave a lift to the other passengers.
But President Cyril Ramaphosa called it an “error in judgment”.
Ms Mapisa-Nqakula had traveled to Harare, the capital of Zimbabwe, for a meeting scheduled to discuss regional issues.
The delegation of South Africa’s ruling party – the African National Congress (ANC) – was meanwhile traveling there for crisis talks with the ruling Zimbabwean party, Zanu-PF, with the aim of helping to fight against the country’s political and economic problems.
But opposition politicians have been extremely critical that she let the ANC delegation hitchhike with her.
Mr Ramaphosa, who on coming to power pledged to clean up the ANC’s reputation after a decade of corruption scandals, said that by giving ANC delegates a lift on the plane, she did not had not acted “in the best interest of good governance”.
As a result, he said he decided to suspend Ms Mapisa-Nqakula’s salary, with the money going to a fund to help fight the coronavirus.
In response, the opposition Democratic Alliance party said Mr Ramaphosa did not go far enough, calling the punishment a slap on the wrist.
The issue could be discussed further in Parliament amid some calls for his sacking.