The decision came after it emerged the initial investigator, Hilton Botha, was facing attempted murder charges.
National Commissioner Riah Phiyega says Lt. Gen. Vinesh Moonoo will take over the investigation.
Phiyega says the Pistorius case "shall receive attention at the national level" and Moonoo will "gather a team of highly skilled and experience detectives."
She says Moonoo is the South Africa police's "top detective."
Botha's future in charge of the investigation into world-famous athlete Pistorius came into doubt after charges of attempted murder were reinstated against him in relation to a 2011 shooting incident, when he and two other police officers allegedly fired shots at a minibus.