Countries in northern Africa have the highest death tolls, led by Egypt (696 deaths from 15 003 cases) and Algeria (575 deaths from 7 728 cases).
South of the Sahara, the highest tolls have been in South Africa (397 deaths out of 20 125 cases) and Nigeria (211 deaths, 7 016 cases).
"For now, Covid-19 has made a soft landfall in Africa, and the continent has been spared the high numbers of deaths which have devastated other regions of the world," said Dr Matshidiso Moeti, the WHO's Africa regional director.
WHO emergencies chief Michael Ryan told a virtual news conference in Geneva that the low number of deaths was "really welcome, and it is a credit to the systems and countries that they are picking up cases and are able to treat".
The Irish epidemiologist said that the picture was varied across Africa, with some countries recording a big rise in cases, and others relatively stable.