The JSE All-share index lost $10.68bn between Thursday and Friday.
"Critics would say having a finance minister serving only two days doesn't bode well for the reputation of South Africa," said Mohammed Nalla, head of research at Nedbank Capital.
"International investors are probably thinking: Why didn't the president make a much more considered decision in the first place?"
Credit agency Fitch downgraded South Africa earlier this month, leaving South Africa just one notch above "junk" status. It said on Thursday that Mr Nene's sacking "raised more negative than positive questions".
'Discipline and prudence'
The presidency's statement said Gordhan's role would include "promoting and strengthening the fiscal discipline and prudence" and "working with the financial sector so that its stability is preserved".
The statement also called for "more inclusive growth and accelerated job creation while continuing the work of ensuring that our debt is stabilised over the medium term".
Gordhan was replaced with Nene in 2014 and moved to the post of minister for cooperative governance and traditional affairs.
South Africa is gearing up for important local elections next year where the African National Congress (ANC) is expected to face stiff competition from the Democratic Alliance in urban areas, including the economic hub of Johannesburg.
The countryside remains an ANC stronghold.
Significant erosion of ANC control in metropolitan power-bases could strengthen Zuma's opponents, especially if South Africans blame him for the failing economy.
Source: Agencies