Police divers have retrieved the vehicle, a VW Polo they have been searching for, from the Hennops River in Centurion, Pretoria.
The divers used a rope and heavy-duty machinery as the search for the missing car led to the latest breakthrough.
They worked alongside SAPS Special Task Force, Search and Rescue South Africa, and SAPS Air Wing.
Latest find is major breakthrough
Bodies of the three constables, Keamogetswe Buys, Boipelo Senoge, and Cebekhulu Linda, were recently located in the river. The vehicle they were travelling in had not been found, bar the front and rear bumpers.
This latest find is bringing closure to the search that began on Thursday morning when the three officers disappeared off radar while driving through Johannesburg to Limpopo, from Bloemfontein.
Police spokesperson, Brigadier Athlenda Mathe, confirmed the vehicle fished out of the Hennops river was indeed the VW Polo the three police officers were travelling in.
She said the VIN on the car registration system matched the one on the VW Polo. She also said a white handbag, keys, and a charger were found in the vehicle.
Mathe was relieved that the breakthrough had been made.
On their way to deployment in Limpopo
Buys, Linda and Senoge disappeared while on an Operation Vala Umgodi deployment in Limpopo.
They were travelling back to work after spending the long weekend with families in Bloemfontein.
The trio had last been seen at the Engen garage on the N1 north in Grasmere, Joburg south.
The investigation led police to the Hennops River, where their bodies were discovered.
It is still unclear how they ended up there.
Police Minister Senzo Mchunu cautioned the public against further speculation. He also offered condolences to the families of the deceased.
Special prayer session in Bloemfontein
Meanwhile, the families of the three constables, Free State premier Maqueen Letsoha-Mathae and other high level provincial officials are holding a prayer session at Hoffman Square in Bloemfontein.
During the six-day search across three provinces — Free State, Gauteng, and Limpopo — police found another two bodies in the Hennops river, which runs between the N1 and N14 highways.
This is a developing story.