At a church ceremony in Berlin, two skulls in glass boxes along with a coffin covered with a Namibian flag were placed in front of the altar ahead of the handover.
The repatriation of the remains is a reminder of Germany's short-lived past as a colonial power in Africa - which included the bloody suppression of a Herero and Nama uprising between 1904 and 1908 that left tens of thousands dead.
"We intend to do something today we should have done many years ago, namely to give back mortal human remains of people who became the first victims of the first genocide of the 20th century," German Lutheran Bishop Petra Bosse-Huber told the fully packed church.
Germany is returning 19 skulls, five full skeletons and bone and skin fragments that were stored in hospitals, museums and universities for decades.
In the early 20th century, German scientists tried to prove the "racial superiority" of white Europeans over black Africans by, for example, analysing the facial features of the skulls, well before Nazi-era scientists conducted similar experiments on Jews and others.
"These skulls tell the story of brutal, godless colonial past and its consecutive suppression of the Namibian people. They say, 'Never again!'" Lutheran Bishop Ernst Gamxamub from Namibia said during his sermon.
It was the third time Germany has returned human remains to Namibia. In 2011, 20 skulls were handed over from Berlin's Charite Hospital. In 2014, both Charite and the University of Freiburg gave back 32 skulls and skeletons.
Historians say German Gen Lothar von Trotha, who was sent to what was then South West Africa to put down an uprising by the Hereros against their German rulers in 1904, instructed his troops to wipe out the entire tribe.
About two-thirds of all Hereros were killed, and the order also affected smaller tribes.
In 2004, then-development minister Heidemarie Wieczorek-Zeul travelled to Namibia and offered Germany's first apology for the massacre, which she said was "what today would be labelled as genocide".
Michelle Muentefering, a deputy foreign minister, told the Namibian delegation earlier this week that "we want to help heal wounds".
Germany and Namibia have been negotiating about possible compensation for the descendants of the victims since 2015. When the remains are returned to Namibia on Thursday, Ms Muentefering will travel along for another round of negotiations in Windhoek.
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