Congo troops end refugee protest - Eastern DR Congo is tense
Barricades set up by the protesters on Friday have been removed and roads have re-opened.
The refugees - who are ethnic Tutsis - are still in Burundi, while officials discuss whether it is safe enough for them to return home.
Some 160 refugees were massacred in the border town of Gatumba last month.
The refugees, who are known as Banyamulenge, had refused an offer to move to camps further inside Burundi, away from Gatumba.
About 350 of them had arrived at the DR Congo-Burundi border, after the Burundi authorities said they wanted to re-open the schools in which they had been staying in time for the beginning of the new academic year.
"They say that since they feel unsafe in Gatumba, they'd prefer to feel unsafe at home, in their own country," said Refugees International's Andrea Lari, who is in Uvira.
￼"And from the DR Congo government's point of view, they've given an undertaking that they cannot prevent Congolese coming back."
The reasons behind the protests remain unclear.
One possible explanation is that the residents of Uvira resent the idea of returning refugees receiving preferential treatment.
Another is that as ethnic Tutsis, they are distrusted after the offensive launched by dissident troops in June to prevent what they described as the planned massacre of Banyamulenge civilians.
A peace deal intended to end DR Congo's five-year war in which an estimated three million people died was signed in 2002.
But rising tensions in the east of the country have led to fears the fragile peace may begin to unravel.