In his ruling, Judge Hans Fabricius said the rights to life, freedom and security, and treatment with dignity and respect, were among those provided for in South African law that "may not be derogated from even in a state of emergency".
All members of the South African National Defence Force (SANDF) and the Johannesburg Metropolitan Police Department (JMPD) who were present or near Khosa's home should be placed on suspension, he ruled. It was not clear how many people the ruling applied to.
Spokespeople for the SANDF, South African Police Service and JMPD did not immediately comment on the ruling.
The SANDF has said previously its members are expected to abide by the law as they enforce the lockdown and any action "outside the law" will not be condoned. The defence minister has expressed regret over the incident.
The judge called on the SANDF and police to develop and publish within days a code of conduct for a state of disaster and to circulate guidelines to the public on circumstances under which force can be used and how to lodge complaints.
The ruling follows a spate of complaints about brutality by the security forces implementing the lockdown.
Wikus Steyl, representing Khosa's family, said soldiers entered Khosa's home after seeing in his yard a cup of what they said was alcohol, sales of which are banned during the lockdown.
Khosa, who had been inside eating dinner, was assaulted and beaten with a rifle and died from what a coroner concluded was blunt force trauma, Steyl said.
The SANDF members are to be placed on suspension with full pay pending the outcome of disciplinary procedures, the judge ruled. The JMPD officers will be suspended while an investigation into accusations of misconduct is launched.
Steyl said the decision was "bitter-sweet" for Khosa's family, who will seek compensation from the government.
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