Kate and Gerry McCann sued ex-police chief Goncalo Amaral, who led the search for their daughter, following claims he made about them in his book.
Madeleine went missing while on holiday in May 2007 and Mr Amaral had suggested the couple had faked her abduction.
The McCanns said they were "delighted" with the ruling but wanted to emphasise the case had never been about money.
In a statement issued by their spokesman Clarence Mitchell, they said: "It was entirely focused on the effect of the libels on our other children and the damage that was done to the search for Madeleine."
The former police officer can appeal against the ruling.
In The Truth Of The Lie, Mr Amaral alleged Madeleine had died in the family's holiday apartment in Praia de Luz in the Algarve, and that her parents had simulated her abduction and hidden her body.
The McCanns, from Rothley in Leicestershire, said the claims exacerbated their anguish and discouraged people from coming forward with information after Madeleine disappeared.
Madeleine went missing in the Portuguese holiday resort of Praia da Luz, aged three.
Mr Amaral, who initially headed the inquiry into Madeleine's disappearance, was taken off the case in October 2007.
His book, published in 2008, has been a bestseller in Portugal.
The McCanns were originally seeking 1.25m euros (almost £900,000) in damages from Mr Amaral, his publisher and a company that produced a documentary based on his book.
In a written verdict, a court in the Portugeuse capital Lisbon ruled Mr Amaral should pay Mr and Mrs McCann 250,000 euros each in damages, plus interest in excess of 100,000 euros (£71,500).
The court also barred Mr Amaral and his publisher from selling the book or issuing further editions. It also barred the producer of the film from selling the rights to broadcast or distribute it.
During the trial, Mrs McCann told the court that when she had first found out about the allegations she was "quite desperate because of the injustice I felt towards my daughter and our family as a whole".
"It was very painful to read and I also felt anxious and fearful because of the damage I felt it was doing here in Portugal," she said.
Portuguese authorities dropped their investigation into Madeleine's disappearance in 2008, but Scotland Yard started a review in May 2011, after Prime Minister David Cameron responded to a plea from the McCanns.
In 2013, the Met Police opened a formal investigation, known as Operation Grange, which remains ongoing.
In June 2014 police officers used dogs to search several sites in the Praia de Luz resort, as well as "ground penetrating radar" to look for disturbed earth, but their searches did not yield any results.
In their statement, the McCanns said: "A lot has changed in the six years since we launched the action and we are pleased that there is still an active investigation in both Portugal and the UK.
"We would like to remind people that there is still an innocent little girl who is missing and that those responsible for her abduction remain at large."

Lengthy time losses for rain ensured the Welsh county had to settle for bowling practice, eight days before their Championship season starts.
David Lloyd and Michael Hogan took two wickets each.
Glamorgan second XI player Jeremy Lawlor hit 50 not out and Academy opener Connor Brown 33.
Meanwhile, South Africa fast bowler Marchant de Lange could still be signed in time for the opening competitive game at Northants.
Seamer Ruaidhri Smith has been ruled out for six weeks with an abdominal tear, while Will Bragg (back), Timm van der Gugten (shoulder) and Graham Wagg (groin) are set to miss their final warm-up friendly against Nottinghamshire on Sunday 2 April.
Glamorgan coach Robert Croft told BBC Wales Sport:
"Any opportunity we get to get in the middle is good, it got some of the competitive juices going though there are percentages to go up against first-class opposition.
"Jacques played well, it's nice for him, for the team and the supporters.
"The three injuries are being monitored day by day, it's unlikely all three will be fit for Northampton.
"We hope as many as possible of them will be fit, but if they're not, the players in those positions have had opportunities throughout pre-season."
A Portuguese court has awarded the parents of missing Madeleine McCann damages of £358,000 after a libel case.
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Glamorgan's opening first-class match of the season against Cardiff MCCU drifted to a tame draw as the students battled to 149-5 on the final day.