The 20 skulls were returned in caskets draped in Namibian flags, after three years of negotiations between authorities from Germany and the Southern African country.
A delegation of 55 Namibians travelled to Berlin to collect them.
The Namibians' remains were given full military honours at a welcoming ceremony marking their arrival at Hosea Kutako International Airport on 4 October 2011.
Namibia's Prime Minister Nahas Angula said: "These mortal remains are testimony to the horrors of colonialism and ... cruelty against our people. May the mortal remains of our ancestors proceed into their homeland."
The 11 Nama and nine Herero skulls have been placed at a local museum for viewing.
Extending a hand of friendship
Ueriuka Festus Tjikuua, a member of the delegation, told reporters in Berlin: "We have come first and foremost to receive the mortal human remains of our forefathers and mothers and to return them to the land of their ancestors.
"We also extend a hand of friendship to Germans and encourage a dialogue with the full participation and involvement of the representatives of the descendants of those who suffered heavily under ... German colonial rule."
The returning of the skulls has been seen as Germany's acknowledgement of what historians call the first genocide of the 20th century.
The German government expressed regret for the atrocities through a statement issued by Deputy Foreign Minister Cornelia Pieper: "We Germans acknowledge and accept this heavy legacy and the ensuing moral and historical responsibility to Namibia.
"The German government is fulfilling this duty through particularly close bilateral cooperation and development cooperation with Namibia."
Germany ruled Namibia, which was then known as South West Africa, from 1884 until1915.
Herero and Nama tribes revolted against colonial rule in 1904, accusing the European settlers of taking their livestock, land and women. The two tribes killed 123 German civilians in days.
In reaction, Germany's General Lothar von Trotha signed an extermination order against tribe members and a bloody war ensued from 1905 to1908.
Local individuals who were not killed were placed in detention and died from various causes, including malnutrition and severe weather.
An estimated 300 tribal members were beheaded and their skulls were taken to Europe for experimentation. This is largely seen as the beginning of Nazi racial theory, which culminated in the extermination of 6-million Jews decades later during the Second World War.
Discovery of the skulls
Some of the Namibian skulls were rediscovered in 2005 at Charite University Hospital in Berlin and at the University of Freiburg in southwest Germany. So far, 59 skulls have been located at the two institutions.
Claudia Peter, spokesperson for the hospital, said: "They thought that they could prove that certain people were worth less than they were. What these anthropologists did to these people was wrong and their descendants are still suffering for it."
From the 80 000 Hereros living in South West Africa before the genocide, only 15 000 remained.
Professor Karl Max Einhaupl, CEO of Charite University Hospital, said: "With this step we face up to an inglorious chapter of German history. As a medical doctor and scientist myself, it is especially painful for me to realise that even physicians worked in the service of this early form of racism."