The Scorpions investigated Mr Zuma for eight years on corruption charges
South Africa's new serious crime squad has begun work six months after its FBI-style predecessor was disbanded amid claims of political bias.
The new unit, to be known as the Hawks, is intended to tackle organised and white-collar crime.
Its predecessor, the Scorpions, pursued several senior figures from the ruling ANC, including Jacob Zuma, who became president in May.
The ANC's opponents said the Scorpions' abolition was a political move.
But critics of the elite crime unit said the investigators were too focused on bringing down members of the ANC.
Mr Zuma's supporters maintained that the corruption charges brought against him were part of a political plot to prevent him becoming president by allies of Mr Zuma's rival, former President Thabo Mbeki.
The charges were dropped in April after a tape-recording emerged which suggested that the prosecution had been politically motivated.
Mr Mbeki has always denied such suggestions.
As well as charges of political bias, the Scorpions unit, which was a part of the justice department, also had notoriously bad relations with the police.
The BBC's Mohammed Allie in Cape Town says the relationship between the two agencies was characterised by jealously and lack of co-operation.
The new Directorate for Priority Crime Investigations should not suffer from similar problems, our correspondent says, because it will operate under the wing of the police services.
However, almost all of the investigators from the Scorpions have moved over to the new unit.
Launching the directorate, Police Minister Nathi Mthethwa said he was encouraged that most of the Scorpions agents had been retained and urged the unit to make a quick impact.
"We expect the unit to zoom in on the activities of criminals and destroy their networks, at home and globally," local news agency Sapa quoted him as saying.
A caseload of 288 investigations was symbolically handed over to the head of the new agency, Anwa Dramat.
Analysts say Mr Dramat, a relatively unknown former deputy police chief of Western Cape province, was a surprise choice for the post.