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...