About 4,000 people stood on the tarmac at the capital Windhoek's international airport, where the plane carrying the skulls home landed at sunrise to ululating women and men shouting battle cries amid banners reading "welcome to our ancestors, our heroes.”
At the far end of the runway, two caskets covered with the Namibian flag were taken out of the plane by officers of the Namibia Defence Force, flanked by an honour guard and accompanied by a trumpet salute.
As the caskets were loaded into a military vehicle, a small group of Herero men drew closer, calling to their ancestors and welcoming them home.
"Our people cry tears as our grandmothers and grandfathers are back on their home soil," said Herero chief Kuiama Riruako.
Riruako was part of the 60-member Namibian delegation that flew to Germany at the end of September to receive the skulls at the Charite University hospital in Berlin.
Kupaha Uazukuani, a deputy fire chief at Windhoek's emergency services administration told The Local the atmosphere was electric and emotional at the ceremony.
“It is very painful, but we are also very happy right now,” Uazukuani said.
Namibian Prime Minister Nahas Angula and several cabinet ministers welcomed the return of the skulls.
"These mortal remains are testimony to horrors of colonialism and Germany's cruelty against our people," Angula said. "The Namibian nation accepts these mortal remains as a symbolic closure of a tragic chapter."
The skulls are among an estimated 300 taken to Germany after a slaughter of indigenous Namibians during an anti-colonial uprising in what was then called South West Africa, which Berlin ruled from 1884 to 1915.
Incensed by German settlers stealing their land, cattle and women, the Herero people launched a revolt in January 1904 with warriors butchering 123 German civilians over several days. The Nama tribe joined the uprising in 1905.
The colonial rulers responded ruthlessly and General Lothar von Trotha signed a notorious extermination order against the Hereros.
Rounded up in prison camps, captured Namas and Hereros died from malnutrition and severe weather. Dozens were beheaded after their death and their skulls sent to German researchers in Berlin for "scientific" experiments.
Up to 80,000 Hereros lived in Namibia when the uprising began. Afterwards,
only 15,000 were left.