McDonalds in a statement confirmed a report in The Star newspaper that Humphrey Mmemezi, an executive of the ruling African National Congress, last year ran a 10,000-rand ($1,200) bill on the credit card at one of the company's restaurants in Pretoria.
But the funds made their way out of the McDonald's account, into another account and finally to an art gallery in Johannesburg, The Star said.
McDonald's operations in South Africa are owned by Cyril Ramaphosa, the former trade unionist who took part in the negotiations that saw the end of apartheid and is now a top businessman.
The fast food giant said the owner-operator "was empathetic to the needs of a friend, the artist" by offering him to use his restaurant's credit card facility to process the transaction.
The artist did not have facilities to receive card payments.
"In hindsight, the owner-operator agrees that this was an innocent error of judgment," said McDonald's.
Mmemezi is the Gauteng provincial housing minister.
His office said while his credit card is used mainly for official business, he has reimbursed for personal transactions.
The opposition has asked the former anti-apartheid activist to explain the transaction. He is yet to do so, according to the paper.
Corruption claims have dogged President Jacob Zuma and his government. Police investigators estimate that graft and negligence costs South Africa up to 30 billion rands a year.
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Good to know; we are not alone in the world!