Zuma told reporters he initially appointed Tito Mboweni for a third five-year term from August but the governor asked to leave in November.
Marcus, a former activist within the ruling African National Congress and currently chairwoman of banking group Absa, served as deputy governor of the Reserve Bank between 1999 and 2004.
Sources said she clashed with Mboweni during her tenure as deputy governor before resigning and some observers speculated at the time she might replace him in 2004.
Analysts said Marcus’ appointment may surprise investors who were mostly expecting Mboweni to stay, but she was well regarded by the financial community.
"She’s highly respected in the market place," said Colen Garrow, economist at investment group Brait.
"She oversaw the foreign exchange regulations (as deputy governor) and she’s actually quite a good administrator. I think the appointment won’t move financial markets. It’s a good appointment."
Former deputy finance minister Marcus, 59, would not comment on policy on Sunday, saying it was premature for her to speak before joining the institution.
"I have re-appointed Mr Mboweni as Reserve Bank Governor. However, he has indicated his wish to leave in November 2009 to pursue other interests," Zuma said.
"Given the indication from Mr Mboweni, I have therefore decided to designate Ms Gill Marcus as Governor of the South African Reserve Bank from November 2009."
Mboweni was respected by markets for efforts to fight inflation. He did not say what he would do after leaving the central bank.
Marcus would not be drawn on future policy.
"I’m sure down the line we will have many debates, but now it’s really just to thank everybody for the enormous confidence you’ve shown in me and the opportunity to serve South Africa," she said when asked if she supported inflation targeting.
The trade union and communist party allies of the ruling ANC have demanded inflation targets be scrapped, and want looser monetary policy than what was the case under Mboweni.
But Zuma said investors should not expect major change, given that the new governor had been involved in setting up the current stance, including inflation targeting, during her previous term at the bank.
"She’s not new … let nobody wonder what’s going to happen. She was there when the policy was made so there’s nothing really new," he said, adding the country’s policies had helped cushion the economy from the global downturn.
Labour federation COSATU, a vocal Mboweni critic, welcomed the change.
"We didn’t have a good relationship with Mboweni and so we are not going to be shedding any tears," Zwelinzima Vavi, general secretary of COSATU, said.
"We welcome the appointment of Gill Marcus and hope that she will bring in fresh air into the institution."
Trade unions had called for big interest rate cuts to drive the economy out of recession and save jobs, but the central bank left its repo rate steady at 7.5 percent at its latest meeting last month after 450 basis points in cuts. Reuters