Belgian Chief Prosecutor Frederic Van Leeuw gave the relatives a small, bright blue box containing the tooth in a televised ceremony, and said legal action they had taken to receive the relic had delivered "justice".
The tooth was to be placed in a casket and flown to what today is the Democratic Republic of Congo, which celebrates Lumumba, who was murdered by separatists and Belgian mercenaries in 1961, as an anti-colonial hero.
Lumumba's son Roland said at a press conference in Brussels Friday that the restitution would allow his family to "finish their mourning".
Lumumba's murder -- and the brutal history of Belgian control of the Congo -- have been enduring sources of pain between the two countries.
A fiery critic of Belgium's rapacious rule, Lumumba became his country's first prime minister after it gained independence in 1960.
But he fell out with the former colonial power and the United States and was ousted in a coup a few months after taking office.
He was executed on January 17 1961, aged just 35, in the southern region of Katanga, with the support of Belgian mercenaries.
His body was dissolved in acid and never found.
But the tooth was kept as a trophy by one of his killers, a Belgian police officer.
The tooth was seized by Belgian authorities in 2016 from the daughter of the policeman, Gerard Soete, after Lumumba's family filed a complaint.
The DRC is set to hold three days of "national mourning" from 27 to 30 June -- its 62nd anniversary of independence -- to mark the burial ceremony in Kinshasa of the remains.
Lumumba's children were also received Monday by Belgium's King Philippe, who this month travelled to DR Congo to express his "deepest regrets" over the colonial past.
Historians say that millions of people were killed, mutilated or died of disease as they were forced to collect rubber under his rule. The land was also pillaged for its mineral wealth, timber and ivory.