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The chief magistrate of Pretoria, Martinus Prins, said he officially accepted findings the 30-year-old died of extensive brain injuries sustained during a scuffle with police on the morning of 7 September.
At the time, he said, Mr Biko was being interrogated by five members of the security police who said he had gone "berserk".
Mr Biko died on 12 September in a cell.
"The court finds the available evidence does not prove the death was brought about by an act or omission involving any offence by any person," he said.
The three-minute ruling ended a dramatic three-week inquest and attracted widespread international condemnation.
About 200 of his supporters held an impromptu demonstration outside, watched by police.
They chanted: "They have killed Steve Biko. What have we done? Our sin is that we are black?"
Mr Biko was arrested on 18 August in Grahamstown for writing inflammatory pamphlets and "inciting unrest" among the black community.
During the inquest, the family lawyer, Sydney Kentridge, argued the young nationalist died after an assault by one or more members of the Port Elizabeth Security Police - which they denied.
Family law suit
They did admit Mr Biko was handcuffed, shackled, and left naked in custody and was driven 750 miles to hospital on the floor of a car.
Eastern Cape security police commander, Colonel Pieter Goosen, in charge of the investigation, suggested Mr Biko may have fallen on the floor during the fight "bumping his head".
The post-mortem examination revealed he sustained five major lesions to the brain, a scalp wound, an inner cut on the upper lip, and abrasions and bruising around the ribs.
The magistrate may publish the reason for his findings within the next two weeks but is not obliged by law to do so.
Mr Biko's widow, Ntsikie, refused to comment but intends to sue Justice and Police Minister Jimmy Kruger for damages.
Stephen Biko, the subject of the film Cry Freedom, is widely seen as the greatest martyr of the anti-apartheid movement.
He gave up studying medicine to devote himself to the "struggle", and founded the Black Consciousness Movement in 1969.
It flourished in the mid 1970s as many ANC leaders were jailed or in exile.
Twenty-two years after his death, South Africa's Truth and Reconciliation Commission, set up to investigate political atrocities between 1960 and 1994, denied amnesty to four former security policemen involved in his custody, as they did with a fifth officer in 1998.
The officers were told his killing was not politically motivated, the requirement for granting amnesty.
Criminal proceedings against the five men were submitted to the attorney general of the Eastern Cape. But in October 2003, South African Justice Ministry officials said the policemen would not be prosecuted because of insufficient evidence. Charges of culpable homicide and assault were also considered, but because the killing occurred in 1977, the time frame for prosecution had expired.
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