The court also ruled Thursday that a trust fund be set up to manage reparations awarded to the more than 4,000 victims. Habré has been ordered to pay millions of dollars in compensation.
The trial against Habré began in July 2015 and was the first in which courts of one country prosecuted the former ruler of another for alleged human rights crimes.
Habré's conviction also was the first of a former head of state by an African court for crimes against humanity.
>> Read more: The trial of Chad's ex-dictator Habré, an inconvenient ally
The Extraordinary African Chambers was created by the African Union and Senegal to try Habré for crimes committed during his presidency from 1982-1990. Its ruling against the former Chadian ruler was seen as a blow to the impunity long enjoyed by repressive rulers on the continent.
Habré's conviction brought closure for relatives of up to 40,000 people killed and many more kidnapped, raped or tortured during his time as president.
His trial marked the first time a country had prosecuted the former leader of another nation for rights abuses, and was seen as a landmark example of African rights abuses being tried on the continent.
(FRANCE 24 with AP and AFP)