The tooth belonged to Patrice Lumumba who served as the first prime minister of an independent Congo in June 1960 before he was deposed in a coup.
He was assassinated in 1961 in an operation which involved several Belgian officials.
Belgium’s King Philippe earlier this month expressed his “deepest regrets” for his nation’s abuses in its African former colony, which suffered horrendously under the direct leadership of King Leopold II.
Following a private ceremony in the presence of relatives of Mr Lumumba during which the federal prosecutor handed over a case containing the tooth, Belgium’s prime minister Alexander De Croo told Congolese officials and Mr Lumumba’s family that the restitution came way too late.
“It is not normal that Belgium held onto the remains of one of the founding fathers of the Congolese nation for six decades,” Mr De Croo said.
He also offered apologies for the role played by his country in the assassination.
Congolese Prime Minister Jean-Michel Sama Lukonde said the return of the relic will be essential for the country’s national memory.
After his assassination in 1961, Lumumba’s body was dismembered and dissolved with acid in an effort to keep any grave from becoming a pilgrimage site.
The tooth was seized by Belgian officials in 2016 from the daughter of the Belgian police commissioner who said he took it after overseeing the destruction of Lumumba’s body.
Two years ago, the federal prosecutor’s office said there is no absolute certainty that the tooth being returned is Mr Lumumba’s since no DNA test could be conducted.
Mr Lumumba’s daughter, Juliana, agreed with Mr De Croo the handover was long overdue.
“Father, our hearts bled for 61 years.” she said during the official ceremony, speaking next to a coffin with a picture of her late father on top of it.
“We, your children, your grandchildren and your great-grandchildren — but also Congo, Africa and the world — we mourned your death without a eulogy.”
Later the coffin was brought outside and draped in a Congolese flag.
Mr Lumumba remains for many in Congo a symbol of what the country could have become after its independence.
Instead, it became mired in decades of dictatorship that drained its vast mineral riches.
Mr Lumumba fell afoul of the US and Belgium when he asked for help from the Soviet Union to help put down a secessionist movement in the mineral-rich Katanga region.
When he was deposed by dictator Mobutu Sese Seko Western powers did little to intervene.
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Even though Mr Lumumba’s killers were Congolese, questions have persisted over how complicit Belgium and the United States may have been in his death because of his perceived Communist ties.
A Belgian parliamentary probe later determined that the government was “morally responsible” for Lumumba’s death.
“Several ministers of the Belgian government of the time bear a moral responsibility for the circumstances that led to this murder,” De Croo said. “A man was murdered for his political convictions, his words, his ideals. For the democrat that I am, it is indefensible. For the liberal that I am, it is unacceptable. And for the human being that I am, it is odious.”
In Belgium, the international protests against racism that followed the death of George Floyd in the United States gave a new momentum to activists fighting to have monuments to King Leopold II removed.
Leopold had plundered Congo during his 1865-1909 reign and forced many of its people into slavery to extract resources for his own profit.
In 1908, he handed it over to the Belgian state, which continued to rule over the colony until it became independent in 1960.