Gordhan has denied any wrongdoing, saying the case is politically motivated.
Gordhan, who announced increased funding for universities in a recent budget speech, was accused of illegally approving an early retirement package for a former tax official who continued to work on contract.
"As Director of the NPA, I do not always reverse a decision unless it is an exception, and this matter was of great public interest", he said.
Blink and you might have missed it, but contained deep inside Finance Minister Pravin Gordhan's mini-budget speech from last week was details on allowances for South African ambassadors living overseas.
The South African rand has risen sharply against the dollar on news fraud charges have been dropped against the country's finance minister. The yield premium paid by South African sovereign bonds over U.S. Treasuries narrowed by 11 bps on the day to 281 basis points, the lowest in almost a month. Mr Gordhan "did not have the requisite intention to act unlawfully". He said he was not responsible for taking the decision to prosecute the minister. Abrahams said that the probe into the unit's actions would continue.
Asked whether he intends apologising to Gordhan, Pillay and Magashula, Abrahams responded: "I certainly do not owe anybody an apology".
"Gordhan should have consulted his deputy Nhlanhla Nene to advise him", he says.
Gordhan, Magashula and Pillay were due to appear in the Pretoria Regional Court on Wednesday, November 2. He called the allegations a political stitch-up, and he has clashed with Zuma over the affordability of nuclear power plants the president wants to build, and the management of state companies and the national tax agency.
"We are profoundly disappointed that Mr Abrahams still does not understand the enormity of what the Hawks and his staff have done, and is still not frank with the public", a statement from the two NGO's said. Gordhan, who served as finance minister from 2009 to 2014, was widely seen as a compromise appointment by Zuma after his surprise move to replace a respected technocrat with an unknown member of parliament.