Andre Hanekom was arrested in August and then accused of being a leader of a jihadist group in northern Mozambique.
His daughter said he had become ill on Saturday in Pemba jail, bleeding from the stomach and convulsing.
He had died before a court hearing this month where he hoped to prove his innocence, Andrie Hanekom said.
Contacted by the BBC, police said they had not been informed of Mr Hanekom’s death and could not comment.
“His family are absolutely broken. We have tried for six months for the world to see he was an innocent man and we have lost him. We were so close – his court hearing was supposed to be this week,” Ms Hanekom told the BBC.
“My father was a good man. He was an amazing father. He was a very, very honest straight-forward person. He did only his best for his family for years in Mozambique and South Africa. I want the world to know that,” she said.
What charges did he face?
In January, months after his detention, the public prosecutor’s office in Cabo Delgado named Mr Hanekom and two Tanzanians as leaders of a jihadist group, which has been terrorising the gas-rich northern province for more than a year.