Police were tipped off on Thursday evening that the woman's body was in a blue Nissan NX100 in Heywood.
On Friday, officers followed a car matching its description which was seen in Claybank Street and later found abandoned on nearby River Street.
Lee Nolan, of Bamford Road, Heywood, has been charged with murder and is due at Bury Magistrates' Court on Monday.
He has been remanded in custody.
A 70-year-old man who was arrested on Friday has been released without charge and no further action will be taken against him, a spokesman from Greater Manchester Police said.
A 48-year-old man has been charged with murder after a woman was found dead in a car boot in Greater Manchester.