The judge ruled that the law contravened the constitution, which guarantees equality for men and women.
Edith Mmusi and her two sisters have fought a five-year legal battle after their nephew said he was the rightful owner of their house.
Correspondents say traditions which stop women from inheriting property exist in many African societies.
Judge Key Dingake said that in the name of fairness and equality women should have the right to inherit property.
“It seems to me that the time has now arisen for the justices of this court to assume the role of the judicial midwife and assist in the birth of a new world struggling to be born,” AFP news agency quotes him as saying.
Edith Mmusi, the only one of the sisters at the High Court in Botswana’s capital Gaborone, was very excited by the ruling.
“It’s a great day for us,” she said.
They first contested their nephew’s claim in a customary court in 2007.
They lost the case and a subsequent appeal before turning to the civil courts.
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