Joe Kappen died from lung cancer in 1991, aged 48, but has become the chief suspect over the rape and murder of the girls at Llandarcy in 1973.
Forensic scientists are to take DNA samples from his remans in a bid to prove his guilt and close one of south Wales' most notorious unsolved murder cases.
After working throughout the night at Port Talbot's Goytre Cemetry, gravediggers removed his coffin at 1455 BST from the plot he shared with two relatives.
It was then taken by pathologists to a local mortuary, where samples were to be taken before a re-burial and short service Saturday.
Police want to check the resulting DNA sample against a profile found at the murder scene three decades ago.
But it could take up to six weeks before scientists have test results, and longer until Mr Kappen's involvement, or otherwise, is proved.
Modern techniques
A nightclub bouncer from Port Talbot, Mr Kappen was amongst 30,000 people interviewed during the original murder hunt.
But South Wales Police has ever brought anyone to justice over the murders.
Modern forensic techniques employed in the inquiry recently established a breakthrough link between the three killings.
The investigation into the Llandarcy murders was re-opened two years ago after a DNA profile of the killer was established from crime scene samples.
One of Mr Kappen's cousins has explained police DNA tests from swabs had already ruled out many suspects still alive and of those men who had died.
Detectives, he claimed, used these to get partial DNA profiles.
Detectives first applied to the Home Office late last year for permission to exhume the body of Mr Kappen.
Earlier in May, his family - who firmly believe in his innocence - asked for the exhumation to be delayed a day as it clashed with the anniversary of the death of Mr Proietti.
Graves restored
The UK's first exhumation of a murder suspect began at 0000 BST with gravediggers first removing the body of Mr Kappen's stepfather Clemente Proielle - buried above him.
Police reassured families that all the graves affected by the two-day operation would be restored exactly as they were found.
But, regardless of the test's outcome, he may never be named as the girls' killer because he never stood trial on any charges.
However, a Home Office review in the light of any new evidence would allow detectives to finally end an inquiry which has remained open for almost three decades.