Luana Ketlan was rushed to hospital suffering from severe abdominal pains before doctors realised she was seven months pregnant, police in Brazil have said.
She was also diagnosed with acute anaemia and delivered a premature baby boy, who survived, after her labour was induced.
However the teenager's health deteriorated after the birth and tests revealed she had a number of complications including low blood pressure, cirrhosis of the liver and water on the lungs.
Luana was being airlifted to a specialist hospital in Manaus 225 miles away (363km) when she died en route.
Police say her dad Tome Faba, 36, had been sexually abusing her for four years and issued a warrant for his arrest after he went on the run.
He was arrested in Coari a week later and has appeared in court charged with child abuse and manslaughter.
Faba's horrified family, who live on the outskirts of Coari, have claimed they were unaware of the abuse.
Coari police chief José Barradas said at a press conference: "The teenager lived with her parents in a rural area outside the city.
'"She did not realise, until two months ago when she began to feel pains in her abdomen, that she was five months pregnant.
"Luana claimed she was ordered to go fishing with her father and was allegedly raped by him while there."
A relative of Luana, who wished to remain anonymous, said she was an innocent and immature schoolgirl who kept the abuse a secret because she was traumatised.
It was only when the slightly-built girl's body started to change that relatives became suspicious that she could be pregnant and uncovered the truth.
When Luana was persuaded by an aunt to reveal who the dad of her baby was her own mum refused to believe her.
Chief Barradas said Faba threatened to kill Luana if she told anyone about the abuse.
He added: "Members of the family tried to step in and protect the child by alerting social services.
"They reported the abuse to police and a warrant was issued for Tome's arrest but before it could be executed Luana's health deteriorated and she died shortly after childbirth."
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