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Battling embarrassment in the glare of a global media spotlight, they named the nation's most senior detective to take over, as preliminary hearings to decide whether the Olympic and Paralympic star can go free on bail were adjourned until Friday.
Hilton Botha, the initial lead investigator had already faced a torrid time over his evidence from defence counsel this week, and police commissioner Riah Phiyega said he might become distracted by the charges relating to the bus shooting in 2011.
"From this point forward, I will take over," Lieutenant General Vinesh Moonoo told Reuters. A 32-year veteran of the force, he added: "It will not affect the court proceedings."
Charges against Warrant Office Botha over the taxi minibus shooting had been dropped but the National Prosecuting Authority told Reuters they were reinstated on Feb. 4 - 10 days before Pistorius shot girlfriend Reeva Steenkamp in his Pretoria home.
"The decision to reinstate was taken on Feb. 4, way before the issue of Pistorius came to light or the murder of Reeva was committed," NPA spokesman Medupe Simasiku told Reuters. "It's completely unrelated to this trial."
It is not clear whether the dismissal of Botha would affect the athlete's chances of securing release from custody pending his trial. After a fourth day of bail hearings, the judge said the court would sit again on the matter on Friday.
At the time of the shooting in 2011, Botha was chasing a man accused of murdering a woman and disposing of her dismembered body down a drain, local media said.
Pistorius, who was born without bones in his lower legs and runs on carbon-fibre racing blades, faces life in prison if convicted of the premeditated murder of Steenkamp in the early hours of Valentine's Day. He denies murder and his lawyers say he opened fire with a pistol at what he thought was a burglar.
Sportswear giant Nike froze its endorsement contract with Pistorius on Thursday saying the athlete should be "afforded due process".
Other companies with sponsorship deals, including British telecoms firm BT, U.S. sunglasses maker Oakley and French designer Thierry Mugler, have declined to comment on their contracts while the bail hearing is continuing.
POLICE UNDER PRESSURE
The revelations about Botha capped a troubling 24 hours for South Africa's prosecution service.
Under cross-examination at the hearing on Wednesday, the detective was accused of contaminating the crime scene in Pistorius's house and backtracked on details like the distance of witnesses from the home when they heard shouts and shots.
Grilled by lead defence counsel Barry Roux, he also had to concede that Pistorius's version of events - that he fired into the toilet door in a blind panic thinking an intruder was lurking behind it - was plausible.
"The poor quality of evidence presented by the chief investigating officer exposed disastrous shortcomings in the state's case." Roux said in arguing for Pistorius's release.
The 26-year-old runner denies murder and was more composed in court after repeatedly breaking down in previous hearings.
His uncle, Arnold Pistorius, said his nephew was eating again after consuming nothing for six days and had spent much of his time in police custody reading the Bible.
A trial is likely to take many months to prepare, and even if he is acquitted, Pistorius faces a huge challenge to rebuild his career and image in the eyes of the millions around the world who saw him as the epitome of triumph over adversity.
At the close of Thursday's arguments, prosecutor Gerrie Nel tried to recapture the initiative, reminding the court of the seriousness of the premeditated murder charges facing Pistorius.
"His actions are indicative of a man who was willing and ready to kill," Nel said. "There were two people in the house.
"One survived to give his version."
SOUTH AFRICA AGOG
The proceedings have gripped South Africans, who have found themselves debating the finer points of police forensics and the ins and outs of the criminal justice process.
As public opinion has swayed back and forth, schoolchildren have come to blows in playgrounds over the athlete's innocence or guilt, and on Thursday "Hilton Botha" was a top-trending topic on Twitter in South Africa.
"We talk about the case every day. It's all over the news. You can't ignore it," said Happy Ngwenya, a taxi driver waiting for rides in Johannesburg's Sandton financial district.
"He must face his music but the thing is, here in South Africa, criminals have so many rights."
With huge international media interest in the case against a global celebrity, many South Africans feel that apparent initial slip-ups by the police are hurting the country's image.
"Bring someone from outside to sort out this mess," said businessman Godfrey Baloyi. "The whole justice system needs an overhaul."