ATHENS—Europe’s top human-rights court ruled on Wednesday that Greece failed to protect a Muslim woman from discrimination, and deprived her of property rights, when it made her follow religious rather than civil law on inheritance.

Chatitze Molla Sali, a 67-year-old widow, appealed to the European Court of Human Rights in Strasbourg, France, claiming she had suffered discrimination after Greece’s highest court ruled that her deceased husband’s will bequeathing his property to her should be ignored and the inheritance should be divided up based on Shariah law.

“Greece was the only country in Europe which, up until the material time, had applied Shariah law to a section of its citizens against their wishes,” the ECHR said in its ruling. It is expected that the Greek state will now have to compensate Mrs. Sali for her lost inheritance.

Greece’s practice of applying Shariah law, which has since January 2018 been made optional rather than obligatory, covers only a small part of its population: the 100,000 Greek Muslims living in Thrace, the northern region near the border with Turkey. The practice dates from the 19th century, when Greece gained its independence after more than four centuries under Ottoman Turkish rule.

Under the 1923 Lausanne Treaty, which settled Turkey’s relations with Europe after World War I, Greece promised to let its Muslim minority live under its own customs, and reserved Shariah for family-related matters such as inheritance, marriage, divorce, alimony and child custody. Greece’s practice continued even after Turkey abolished Shariah in 1924 as part of Mustafa Kemal Atatürk’s push to modernize Turkey.