Judges made it clear in their decision their job was not to decide whether the McCanns bore any criminal responsibility over their daughter's disappearance and it would be wrong for anyone to draw any inferences about the couple's guilt or innocence from their ruling.
But they added: "It should not be said that the appellants were cleared via the ruling announcing the archiving of the criminal case.
"In truth, that ruling was not made in virtue of Portugal's Public Prosecution Service having acquired the conviction that the appellants hadn't committed a crime.
"The archiving of the case was determined by the fact that public prosecutors hadn't managed to obtain sufficient evidence of the practice of crimes by the appellants.
"There is therefore a significant, and not merely a semantic difference, between the legally admissible foundations of the archive ruling.
"It doesn't therefore seem acceptable that the ruling, based on the insufficiency of evidence, should be equated to proof of innocence."
Highlighting the McCanns' Tapas Nine friend Jane Tanner's much-questioned sighting of the suspected 'abductor', they added: "It's true that the aforementioned criminal inquiry ended up being archived, namely because none of the apparent evidence that led to the appellants being made 'arguidos' was subsequently confirmed or consolidated.
"However even the archive ruling raises serious concerns relating to the truth of the allegation that Madeleine was kidnapped."
The McCanns were told their 'arguido' status had been lifted on July 21 2008 when the Portuguese probe into Maddie's disappearance was shelved, three days before the controversial book was published.
The former detective was ordered to pay the couple £430,000 by a Lisbon court in April 2015 after they won round one of their lengthy judicial battle.
Mr Amaral got that ruling - and a ban on selling his book - overturned on appeal in April last year.
The decision by Lisbon's Court of Appeal sparked the Supreme Court fight which was resolved last Tuesday.
The Supreme Court judges said the McCanns claimed the book and a TV documentary based on the book would have damaged the honour and good name of any "innocent person who had been cleared through the shelving of the criminal investigation."
It is believed the McCanns are discussing the possibility of taking the case to the European Court of Human Rights.
Madeleine was three years-old when she disappeared from a holiday apartment in Praia de Luz, Portugal, on May 12, 2003.
British police have spent more than £10 million looking for Madeleine.
A spokesperson for the McCann's did not want to respond to request for comment last night.