Hilton Botha, who took the stand against Pistorius at the Paralympic and Olympic track star's bail hearing earlier this week, is due to appear in court in May over the 2011 shooting incident, police spokesman Brigadier Neville Malila said.
"Botha and two other policemen allegedly tried to stop a minibus taxi with seven people. They fired shots," Malila told Reuters.
At the time, Botha - a detective with 24 years on the force - was chasing a man accused of murdering a woman and disposing of her dismembered body down a drain, local media said.
The charges against Botha were provisionally withdrawn but were reinstated on February 4 - 10 days before the shooting of 29-year-old model and law graduate Reeva Steenkamp in a locked toilet at Pistorius' Pretoria home, the National Prosecuting Authority (NPA) said.
"The decision to reinstate was taken on February 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."
Malila said now that the court had decided to charge Botha, there would be an internal disciplinary investigation which would decide whether to keep him on the case: "At this stage there are no plans to take him off the Pistorius case."
It was unclear why the charges were reinstated against Botha, or how the latest twist in Pistorius' sensational four-day bail hearing will affect the athlete's chances of securing release from custody pending his trial.
Pistorius, a double amputee dubbed "Blade Runner" because of his carbon fiber racing blades, faces life in prison if convicted of the premeditated murder of Steenkamp in the early hours of Valentine's Day.
The revelation about Botha capped a troubling 24 hours for South Africa's prosecution service.
Under cross-examination at the bail hearing on Wednesday, the lead detective was accused of contaminating the crime scene in Pistorius's house and had to backtrack on details such as the distance of witnesses from the athlete's home.
Grilled by lead defense counsel Barry Roux, he also had to concede that Pistorius's version of events - that he fired into the toilet door thinking an intruder was lurking behind it - was plausible.
Pistorius, 26, has denied murder.
SOUTH AFRICA AGOG
The bail hearing resumed on Thursday with prosecutors immediately admitting they had only just found out about the charges hanging over Botha.
The proceedings have gripped South Africans, who in 48 hours have become self-appointed experts on the finer points of police forensics and the ins and outs of the criminal justice process.
"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 the heart of Johannesburg's Sandton financial district.
"He must face his music but the thing is, here in South Africa, criminals have so many rights."
With massive international media interest in the case against a global star, many South Africans feel the justice system's apparent shortcomings hurt country's image in the eyes of the world.
"Bring someone from outside to sort out this mess," said businessman Godfrey Baloyi. "The whole justice system needs an overhaul."