The case, in a rural area near the provincial capital Bukavu, signals the spread of an outbreak that experts believe circulated undetected for around two months in Ituri province, several hundred kilometres to the north, before being identified last week.
The outbreak has been linked to 139 deaths, with 600 suspected cases reported in Ituri and North Kivu provinces as of Wednesday, according to the World Health Organisation.
Two cases have also been confirmed in neighbouring Uganda.
The Alliance Fleuve Congo, which includes the Rwanda-backed M23 rebels who seized swathes of eastern DR Congo last year, said that the 28-year-old patient had died and been buried safely.
It said the individual had travelled from the northern city of Kisangani but gave no details of recent movements.
South Kivu health spokesman Claude Bahizire told Reuters earlier on Thursday that two suspected cases had been detected in the province, including the fatal case.
The other patient was in isolation awaiting test results, he said.
An Ebola case was also confirmed last week in Goma, the capital of neighbouring North Kivu province, which is under M23 control.
The WHO declared the outbreak of the virus' Bundibugyo strain, for which there is no vaccine, a public health emergency of international concern over the weekend.
Jane Halton, chair of the Coalition for Epidemic Preparedness Innovations (CEPI), said the confirmed cases likely represent only "the top of the iceberg".
CEPI, which funds vaccine development, is assessing potential candidates for Ebola.
She said it may be possible to meet CEPI's target of having a safe, effective vaccine for major outbreaks within 100 days, although this would be "a big lift".
Efforts to contain the outbreak have been complicated by its spread in densely populated urban areas and ongoing armed conflict in eastern DR Congo.
A 2018-2020 outbreak of the Zaire strain in the region was the second-deadliest on record, killing nearly 2300 people.
This time, first responders say they lack basic supplies, which some have attributed to foreign aid cuts by major donors that have weakened local health services and disease surveillance.
The United Kingdom said on Thursday it was allocating up to 20 million pounds ($A38 million) to the response.
The United States, which gave about $US600 million ($A840 million) to the 2018-2020 response, has so far committed $US23 million and said on Tuesday it would help open up to 50 clinics in DR Congo and Uganda.
Uganda's health ministry said late on Wednesday it had not been consulted by the United States on plans to establish clinics, and stressed there is no known local transmission.
Information Minister Chris Baryomunsi told Reuters the US was "overreacting" by banning most travellers from Uganda, along with DR Congo and South Sudan, earlier this week.
"We've handled cases of Ebola at other epidemics for a number of years," he said.
"There is capacity within the country to contain these epidemics."
