Sergeant Gary Silk and Senior Constable Rodney Miller were ambushed and killed in the early hours of August 16, 1998 while staking out armed robbery targets.
Bandali Debs is serving a life sentence for their murders.
Roberts was convicted alongside Debs and jailed for a minimum 35 years in 2003.
But a fresh trial was ordered for the now 41 year old after allegations of police wrongdoing were investigated by Victoria's anti-corruption watchdog, IBAC.
Three appeal judges found long-undisclosed conduct by one particular officer had corrupted Roberts' initial trial.
Senior Constable Glen Pullin destroyed an original statement made about the murders and substituted it with a backdated document, containing dying declarations of Sen Const Miller about there being a second offender.
He then committed perjury, lying about its existence in what the judges labelled a "gross and fundamental corruption of the trial process".
After hearing months of evidence from dozens of witnesses in a Victorian Supreme Court trial, jurors returned their not guilty verdict on Monday.
They had been staying together at an undisclosed location to keep them away from any outside influence while they made their decision.
In an unusual move, jurors began deliberating on Thursday and continued through the weekend.
Justice Stephen Kaye said the trial was one of the hardest he had seen a jury consider, given the length and density of evidence.
"This case has involved an enormous responsibility on each of your shoulders," he said, before dismissing them.
Among the evidence they considered was that of Roberts himself.
He confessed that when police came for him for the murders of two of their own he lied to protect himself.
He told them he knew nothing about the shooting murders and denied being involved in robberies with Debs.
"I knew what (Debs) had done and I didn't want to be dragged into it," he told jurors.
"I lied because Ben killed two police officers. That's not a small thing."
Roberts, who pleaded guilty to 10 armed robberies with Debs, was 17 when he did the first robbery - getting involved while dating the four-time killer's daughter Nicole.
He said he got up during the night and saw Debs with a gun, listening to a police scanner.
Debs, he said, told him in detail about a "shoot out" with the officers.
Debs also gave evidence at the trial, claiming Roberts was with him at the Silky Emperor and it was Roberts who fired the first fatal shot at Sgt Silk when their car was pulled over in Cochranes Road in Moorabbin.
Debs, giving evidence from Goulburn Prison in NSW, rejected suggestions his evidence was designed to minimise his own role in what prosecutor Ben Ihle QC called "low and callous acts".
Debs was labelled a "vile and evil person, a psychopath and liar" by Roberts' barrister David Hallowes, who told jurors the evidence could not be trusted.
Sergeant Helen Poke said she won't forget the words Sen Const Miller uttered as she cradled his head in her lap, comforting her dying colleague: "Get them, I'm f***ed, two offenders, one on foot, six foot, dark hair, checked shirt, dark Hyundai".
Lou Gerardi, who sped at 150km/h to get to the scene after radio reports of officers down, said he held Sen Const Miller's hand as he told him to "get them c***s".
Sgt Silk died at the scene, Sen Const Miller died in hospital.
Mr Ihle told jurors if they were to find Roberts guilty they must be satisfied there were two offenders, that Roberts was one of them and that he was criminally involved in the murders.
Roberts is now a free man.
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