Islamic extremists destroyed more than 4000 manuscripts, some dating back to the 13th century, after they seized Timbuktu in 2012, according to the findings of a United Nations expert mission.
They also destroyed nine mausoleums and a mosque's door — all but one of the buildings on the UNESCO World Heritage list.
The majority of the documents dating back to the 13th century — more than 27,000 — were saved by the devotion of the Timbuktu library's Malian custodians, who carried them out of the occupied city in rice sacks, on donkey carts, by motorcycle, by boat and four-wheel drive vehicles.
The first batch of the manuscripts were brought to Timbuktu by plane from the capital of Bamako on Monday.
Authorities said that the return was necessary to protect them from the threats of Bamako's humidity.
The shipment consisted of more than 200 crates and weighed some 5.5 tonnes.
The rest would be shipped in the coming days, officials said.
About 706 kilometres from Bamako, Timbuktu sits on the edge of the Sahara Desert and has a dry climate.
For years, the local municipal and religious authorities have asked for the return of the manuscripts.
Diahara Touré, Timbuktu's deputy mayor, said the famous documents are important to the local people as they "reflect our civilisation and spiritual and intellectual heritage".
In February, the military government committed to return the manuscripts, according to Bouréma Kansaye, the Malian Minister of Higher Education.
He described them as a "legacy that bears witness to the intellectual greatness and crossroads of civilisation" of the city of Timbuktu — "a bridge between the past and the future".
"We now have a responsibility to protect, digitise, study, and promote these treasures so that they continue to enlighten Mali, Africa, and the world," Kansaye said during Monday's return ceremony.
The manuscripts, which UNESCO has designated as part of the World Cultural Heritage, cover a myriad subjects, from Islamic theology and jurisprudence, astronomy, medicine, mathematics, history, and geography.
They are a testimony to the rich cultural heritage of the Mali and Songhai empires in West Africa.
Mali, along with neighbouring Burkina Faso and Niger, has long battled an insurgency by armed militants, including some allied with al-Qaida and the Islamic State group.
Following two military coups, the ruling junta expelled French troops and instead turned to Russia for security assistance.
Still, 13 years after the occupation of Timbuktu, the security situation in Mali remains precarious and analysts say it has worsened in recent months.
Although the city is back under government control, militants continue attacking its surroundings, including as recently as last month.
