The minister had earlier rebuked Dudu Myeni, chairwoman of state-owned South African Airways and a close ally of Zuma, for mismanaging a 1 billion rand ($62.98 million) deal with Airbus.
South African President Jacob Zuma on Saturday denied rumours he had an affair with the chairwoman of state-owned airline amid media speculation the relationship had led to the sacking of the finance minister.
Zuma dismissed Finance Minister Nhlanhla Nene on Wednesday. The minister had earlier rebuked Dudu Myeni, chairwoman of state-owned South African Airways and a close ally of Zuma, for mismanaging a 1 billion rand ($62.98 million) deal with Airbus.
Myeni is also executive chairwoman of Zuma's charitable trust, the Jacob Zuma Foundation.
"Her relationship with the President is purely professional, and is based on the running of the Foundation," the Presidency said in statement. "Rumours about a romance and a child are baseless and are designed to cast aspersions on the President."
Zuma replaced Nene with a relatively unknown parliamentarian, David van Rooyen, unnerving investors in an ailing economy whose investment grade status is already at risk.
Citing an unnamed government official, Business Report newspaper reported this week that Nene's dismissal could be linked directly to his fall-out with the SAA board.
Many other local media had also speculated Nene might be moved out after he rebuked Myeni.
Rumours of a romantic relationship between Zuma and Myeni have circulated since 2009 when the she was appointed to the board of the ailing national flag carrier.
Zuma's office also criticised as a "malicious fabrication" reports that Nene was removed because Myeni was not happy with instructions from the respected former finance minister.
"No member of the SAA Board is above the Minister of Finance or can operate outside of the mandate and direction provided by the Minister of Finance and the National Treasury," the Presidency said.
Zuma, South Africa's leader since 2009, is a polygamist married six times and father of more than 20 children
The axing of Nene, a veteran civil servant who was keen to rein in government spending in Africa's most industrialised economy, has sent the rand to record lows and caused a sell-off in banking stocks.
Nene was also opposed to plans to spend possibly as much as$100 billion building a fleet of nuclear power stations, an investment most analysts said the country could not afford. Former South African health minister and leading anti-apartheid activist Barbara Hogan called on Friday for Zuma to quit.
The highest-profile member of the African National Congress (ANC) to come out against the sacking of Nene, Hogan said Zumahad crossed a line and needed to be held to account for the dismissal of a respected long-term finance ministry official.