Officers have arrested two men, aged 70 and 48, who remain in custody on suspicion of murder.
Greater Manchester Police (GMP) were tipped off that the woman's body was in a blue Nissan NX100 in Heywood, shortly after 19:35 BST on Thursday.
On Friday, officers followed a car matching its description, which was seen in Claybank Street at 15:50 BST.
It was later found abandoned on nearby River Street.
A post-mortem examination and formal identification of the victim is yet to take place, police said.
Det Supt Tony Creely, from GMP, said: "Understandably an incident like this has caused a lot of concern in the community and interest in the media, but I would like to assure everybody that a thorough investigation has been launched.
"I would like to urge anybody with any information to please come forward."
Police are appealing for witnesses after a woman was found dead in a car boot in Greater Manchester.