The man died on Wednesday after spending several days at home with his large family while showing symptoms.
This is the first transmission of Ebola inside Goma, a city of more than two million people on the Rwandan border, a scenario that health experts have long feared.
The painstaking work of finding, tracking and vaccinating people who had contact with the man – and the contacts of those contacts – has begun.
“We’re seeing the first active transmission chain in Goma and expect more to come,” the International Rescue Committee’s Ebola response director, Andre Heller, warned in a statement.
This outbreak has killed more than 1,800 people, nearly a third of them children.
It is now the second-deadliest Ebola outbreak in history, and last month the World Health Organisation (WHO) declared it a rare global emergency.
Rwanda’s state minister for foreign affairs Olivier Nduhungirehe confirmed the border closure, a day after WHO officials praised African nations for keeping their borders open.
Last week Saudi Arabia stopped issuing visas to people from DR Congo while citing the Ebola outbreak, shortly before the annual hajj pilgrimage there this month.
DR Congo’s presidency swiftly condemned Rwanda’s decision, and people at the busy border expressed frustration.
“I can’t understand why they don’t just test us instead of closing these borders,” said Angel Murhula, who works in Rwanda.
WHO has recommended against travel restrictions amid the outbreak but says the risk of regional spread is “very high.” Rwanda, Uganda and South Sudan have long begun vaccinating health workers.
The death on Wednesday in Goma “in such a dense population centre underscores the very real risk of further disease transmission, perhaps beyond the country’s borders, and the very urgent need” for more global support, United Nations agencies said in a joint statement marking a year of the outbreak.
The man in his 40s was a miner returning from an area of northeastern Ituri province, Mongwalu, where no Ebola cases in this outbreak have been recorded, WHO said.
He was exposed to the virus along the roughly 300-mile-long route from Komanda to Goma as he took motor taxis over a number of days through the densely populated region at the heart of the outbreak.
The man arrived in Goma on July 13 and started showing symptoms on July 22.
He was isolated at an Ebola treatment centre on Tuesday.
He had spent five days being treated at home and then went to a health facility, where Ebola was suspected. Symptoms can start to occur between two and 21 days from infection.
“He may not even have been aware of the exposure that he had,” WHO emergencies chief Dr Michael Ryan said.
Symptoms such as fever can be confused with malaria, which is endemic in the region.
DR Congo’s new Ebola response co-ordinator, Jean-Jacques Muyembe, has said there appears to be no link between the case and the previous one in Goma announced two weeks ago. That case was a 46-year-old preacher who managed to pass through three health checkpoints.