The decision by Hilton Botha to quit on Thursday followed criticism for his handling of the probe into Pistorius' shooting of his girlfriend Reeva Steenkamp, as well as the revelation that he faced attempted murder charges for a 2011 case.
He had already been pulled out of the investigation of the February 14 killing at the Olympics and Paralympics star's home.
Police spokesman Neville Malila said Botha voluntarily applied to leave the service after 24 years, and that police would not divulge his reasons.
Botha made several errors as the lead investigator after the double-amputee athlete shot Steenkamp at his home in Pretoria, the South African capital.
He walked through the crime scene without wearing protective shoe covers, potentially contaminating the area; gave conflicting estimates of the distance of the house of a potential witness; and was criticised by the judge in the athlete's bail hearing for failing to secure data from cellular telephones found at the scene of the shooting.
It later emerged that Botha faced attempted murder charges for a case in which he and two other officers fired on a vehicle in an attempt to make it stop. His superiors then removed him from the Pistorius case, replacing him with a senior investigator, police Lieutenant General Vinesh Moonoo.
Pistorius, who was freed on bail, said he mistook Steenkamp for an intruder when he shot her through a locked bathroom door. Prosecutors believe the shooting happened after the couple got into an argument.
Pistorius' next court appearance is scheduled for June 4.
