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The decision by a Lisbon court came after a complaint by Madeleine's parents, Gerry and Kate McCann, their lawyer Isabel Duarte told AFP.
Amaral's book has also been adapted for television.
The former Algarve police chief backed up his claim citing the investigation launched into the parents in September 2007.
Amaral was taken off the case a month later and the McCanns were cleared by a Portuguese court. Portuguese police have since said they are no longer actively investigating.
In Wednesday's ruling the court said the publisher and author must not "quote, comment or analyse ... any part of the book or video that defends the assumption of the death or concealment of (Madeleine's) body."
Madeleine was three and a half years old when she disappeared from her room in the Algarve resort of Praia da Luz on May 3, 2007.
In Britain, the McCann family welcomed the court's decision, saying the "awful claims" in the book "caused our family incredible distress."
"Mr Amaral's central thesis has no evidence whatsoever to support it," the family said in a statement.
"To claim, as he did, that Madeleine is dead, and that we, as her parents, were in some way involved with her disappearance has caused our family incredible distress and it continues to do so."
Separately, Gerry McCann said claims that Madeleine was dead could hamper the search for his daughter.
"There's a lot of people in Portugal, who might have evidence, that believe Madeleine is dead," he told reporters.
"If people believe that, they won't search for her and they won't come forward with information.
"I know for a fact people have been told Madeleine is dead. There is no evidence to support that and that is unforgivable."
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Amaral's book has also been adapted for television.
The former Algarve police chief backed up his claim citing the investigation launched into the parents in September 2007.
Amaral was taken off the case a month later and the McCanns were cleared by a Portuguese court. Portuguese police have since said they are no longer actively investigating.
In Wednesday's ruling the court said the publisher and author must not "quote, comment or analyse ... any part of the book or video that defends the assumption of the death or concealment of (Madeleine's) body."
Madeleine was three and a half years old when she disappeared from her room in the Algarve resort of Praia da Luz on May 3, 2007.
In Britain, the McCann family welcomed the court's decision, saying the "awful claims" in the book "caused our family incredible distress."
"Mr Amaral's central thesis has no evidence whatsoever to support it," the family said in a statement.
"To claim, as he did, that Madeleine is dead, and that we, as her parents, were in some way involved with her disappearance has caused our family incredible distress and it continues to do so."
Separately, Gerry McCann said claims that Madeleine was dead could hamper the search for his daughter.
"There's a lot of people in Portugal, who might have evidence, that believe Madeleine is dead," he told reporters.
"If people believe that, they won't search for her and they won't come forward with information.
"I know for a fact people have been told Madeleine is dead. There is no evidence to support that and that is unforgivable."
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