The 48-year-old man and 33-year-old woman, who are believed to be related to the child, were held on Wednesday, almost four months after the discovery of the baby by a dog walker in woodland in Heywood, near Rochdale, on April 4.
Officers have been carrying out extensive inquiries including DNA analysis to find out exactly what happened to the child, who was named Pearl by detectives.
The two suspects have been arrested on suspicion of murder, concealing a birth and preventing a lawful burial.
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They remain in custody for questioning and inquiries are ongoing, a spokesman for Greater Manchester Police (GMP) said.
Detective Superintendent Lewis Hughes, who is leading the investigation for GMP, said: "This continues to be an incredibly heart-breaking case for everyone involved - from the detectives working painstaking hours to find those responsible to members of the public that have felt the loss of Pearl.
"While we have two people in custody, our investigation is still very much ongoing and I would continue to urge anyone with even the smallest piece of information - no matter how insignificant it may seem - to please get in touch.
"We're committed to finding the truth for this little girl and truly believe the public could hold the key to this tragic case."
The baby was found in a remote area of Roch Valley Woods, which is popular with dog walkers and families, at around 7.10am on April 4.
Forensic examinations determined she was born with a congenital defect that resulted in her missing two ribs, was probably newborn and likely to be Caucasian, although mixed heritage cannot be ruled out.
She was found abandoned, unclothed, with no blanket or nappy.
Detectives drafted in a behavioural psychologist and made numerous public appeals for information to try to identify her.
Anyone with information is asked to contact police on 0161 856 4810 or 07387 705768 quoting incident number 368 of 04/04/18.
Reports can also be made anonymously through the independent charity Crimestoppers on 0800 555 111.