The judge convicted him of rape, sexual slavery and ordering killings during his rule from 1982 to 1990.
Victims and families of those killed cheered and embraced each other in the courtroom after the verdict was given.
It was the first time an African Union-backed court had tried a former ruler for human rights abuses.
Habre has been given 15 days to appeal.
"Today will be carved into justice as the day that a band of unrelenting survivors brought their dictator to justice," said Reed Brody from Human Rights Watch, who has worked on the case for 17 years and was in court for the judgement.
Throughout the trial, Habre refused to recognise the court's legitimacy, frequently disrupting proceedings.
The ex-president denied accusations that he ordered the killing of 40,000 people during his rule from 1982 to 1990.
His critics dubbed him "Africa's Pinochet" because of the atrocities committed during his rule.
Survivors had recounted gruesome details of the torture carried out by Habre's feared secret police.
One of the most notorious detention centres in the capital N'Djamena was a converted swimming pool.
Witnesses said victims endured electric shocks, near-asphyxia, cigarette burns and having gas squirted into their eyes.
Some were subjected to "supplice des baguettes" (torture by sticks), when the victim's head is put between sticks joined by rope which is then twisted.
Gberdao Gustave Kam, president of the special court, said Habre had also committed three acts of rape.
Habre was arrested in Senegal, where he was exiled, in 2013.
Many of his victims campaigned for him to be tried following his overthrow in 1990.
In 2005, a court in Belgium issued a warrant for his arrest, claiming universal jurisdiction but, after Senegal referred the issue to the African Union, the AU asked Senegal to try Mr Habre "on behalf of Africa".
In 2013, a court in Chad sentenced him to death in absentia for crimes against humanity.