The minerals include cassiterite, or tin ore, as well as coltan, used in devices such as mobile phones.
The return of the materials follows new international regulations aimed at cleaning up the mineral sector.
DR Congo's mineral wealth has been a major factor in years of conflict.
Armed groups - local and foreign - have seized control of many mines in the east, bordering Rwanda and few Congolese have benefited from their country's vast mineral wealth.
Rwanda has twice invaded DR Congo saying it was fighting rebel groups based there but its army has been accused of looting minerals during the conflict in which an estimated five million people died.
Rwanda's Natural Resources Minister Stanislas Kamanzi handed the minerals - loaded in five lorries - to Congolese authorities at a ceremony in the border town of Gisenye.
BBC East Africa correspondent Will Ross says the handover is a sign of the greatly improved relations between two countries that have often been bitter enemies.
"I think it [reflects] the spirit of cooperation between the two countries," DR Congo mining ministry adviser, Paul Mabolia Yenga, told the BBC's Network Africa programme.
Rwanda's deputy director of natural resources Michael Biryabarema said Kigali wanted to end perceptions that it benefited from illegal mining in DR Congo.
"It's a lie that has gone for a long time," he said.
He said Rwanda and DR Congo would work together to strengthen their mining sectors.
"We are more interested in... the development of our industry, bilateral relations and the establishment of proper trade relations," Mr Biryabarema said.
Rwanda has for years been a major conduit for conflict minerals from DR Congo, correspondents say.
It long denied any involvement but now supports efforts to make the trade more transparent.
Any seized minerals without the sign would be returned, Mr Biryabarema said.
"I think we've set a precedent... but preferably they will not be allowed into the country if they have not been tagged," Mr Biryabarema said.
The landlocked country has mineral deposits within its own borders and wants to label them conflict-free, our correspondent says.
But as Rwanda stands to lose out on vast revenues from the trade in Congo some analysts question just how rigorous the authorities there will be.
Earlier this week, a website was launched to promote transparency in the Congolese mining sector.
The Carter Center said www.congomines.org would give people more information about the mining sector, including contracts and payments.
Hundreds of mining documents and maps will be published on the site, it said.
But Congolese state-owned mining giant Gecamines would not release confidential contracts without the permission of its joint venture partners, CEO Kalej Nkand said, Reuters news agency reports.
"The proposed publication of these contracts has no legal basis. It is doubtful that our partners would consent to it," he is quoted as saying.