Senior government officials including Prime Minister Apollinaire Kyelem de Tembela joined around a hundred relatives who gathered in the capital by 13 coffins draped in the national flag.
"We are happy that our martyrs can finally rest in peace with a fitting grave because their souls had been wandering for eight years," said Joseph Saba, a representative of the 13 families.
"It's a historic day, a solemn moment. They were killed, but they (the assassins) didn't kill the vision, they didn't snuff out the mission," a chaplain said on Wednesday after the blessing of the bodies.
Benewende Sankara, a lawyer for the Sankara family with no relation to them, said the ceremony was "the culmination of the quest for justice."
Sankara's widow Mariam Sankara and his two children, who opposed the choice of location for the burial, were absent, but other family members attended the ceremony, AFP journalists saw.
At its conclusion, the coffins were then placed in tombs behind a giant statue of Sankara erected at the site of his murder.
The government has said an international ceremony will be organized on October 15 this year to honor the victims.
A Marxist-Leninist Pan-African icon and a hero of anti-imperialist causes, Sankara seized power in a 1983 coup and was gunned down with a dozen other leaders in another putsch led by his number two Blaise Compaore on October 15, 1987.
The bodies were initially buried on the outskirts of Ouagadougou and exhumed in 2015 for a judicial investigation.
Sankara came to power in August 1983 as an army captain, aged just 33.
Nicknamed Africa's Che Guevara, he blasted the West for neo-colonialism and hypocrisy and carried radical reforms.
He changed the country's name from the colonial-era Upper Volta to Burkina Faso - "the land of honest men" - and pushed through a range of changes, including promoting vaccination and banning female genital mutilation.
Compaore, his successor and former comrade-in-arms, remained in power in the West African nation until a popular uprising ousted him in 2014.
A Burkinabe court convicted Compaore to life in prison in absentia last year for his role in the assassination.