President Thabo Mbeki's African National Congress rules in a formal alliance with the SACP and the South African Congress of Trade Unions, Cosatu.
Mr Nqakula has been handed one of the most difficult jobs in South Africa.
The murder rate of 59 per 100,000 residents is among the highest in the world.
Lowering crime levels is crucial to attracting foreign investment and tourists and persuading skilled professionals to remain in South Africa, says Reuters news agency.
Click here to see international murder rates
He was promoted from Deputy Minister of Home Affairs - a portfolio taken by his wife, Nosiviwe Mapisa-Nqakula, the ANC's chief whip in parliament.
Mr Tshwete died on 26 April from complications following back surgery. He was buried over the week-end.
Mr Nqakula is a former journalist and poet.
Publicity-shy
Following his appointment, he said that he no sympathy for the argument that poverty forces people into crime.
"There are so many people out there who come from backgrounds of
poverty that continue to be poor, but they don't turn to crime," he said.
A long-time associate, who did not wish to be named, told Reuters news agency that the communist leader was hard-working and publicity-shy.
"Whilst the police will be able to count on the strong support they are used to, we won't see the sort of statements that we got from Tshwete, which some saw as disregard for the constitutional protection of victims and accused," he said.
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