The case has pitted Africa's last hunter-gatherers against one of the continent's most admired governments in a dispute over land that is rich in diamonds and eyed by developers.
Bushmen's ancestors have lived in the Kalahari for thousands of years, and the plaintiffs say they are being forcibly ejected from the game reserve and resettled in camps where their traditional way of life is dying.
The Bushmen, backed by western rights groups, argued their expulsion was designed to increase Botswana's output of diamonds - already its top export - a charge the government denies.
Al Jazeera's southern Africa correspondent Kalay Maistry said: "They are now free to return ... and won't need to get licences in order to continue hunting.
"But the terms and conditions ... have yet to be ruled on ... and the state does have the right to lodge an appeal."
Maruping Dibotelo, Botswana's Chief Justice, delivering his opinion ahead of the final verdict, had argued the case should be dismissed on the grounds that the state owns the Kalahari desert land.
"The contention of the applicants that the government unlawfully deprived them of their land ... must fail," Dibotelo said.
But Judge Unity Dow disagreed, saying Botswana's government had "failed to take account of the knowledge and the culture" of the Bushmen when it expelled them.
"In 2002 they were dispossessed forcibly, unlawfully, and without their consent," he said.