Goma, a lakeside city with a population of two million people, is close to the Rwanda border - more than 354 km (220 miles) south of where the second-largest Ebola outbreak was first detected a year ago.
In another tweet, Ghebreyesus said that 3,000 health workers in Goma had been vaccinated, and that the sick pastor is being treated in the Ebola Treatment Center in Goma, run by the DRC Ministry of Health and Doctors without Borders.
The two people killed, who were community workers near Mukulia in North Kivu province, had been receiving threats since December and one had been attacked previously, the ministry said in a statement.
The UN's World Health Organization had been hopeful it would be able to contain the latest epidemic, thanks in part to a new vaccine.
The health ministries in Congo's neighbors have been preparing for months for the possibility of cases, and frontline health workers already have been vaccinated.
"The identification of the case in Goma could potentially be a game-changer in this epidemic", Tedros warned.
Almost 700 were cured, and total of 160,239 people have been vaccinated against the highly contagious haemorrhagic fever, it added.
Two more Ebola workers were murdered in their homes in the North Kivu town of Beni, the ministry said.
But efforts to roll back Ebola have been hampered by insecurity in a region plagued by militia groups, who have attacked treatment centres.
Now health authorities along his route are trying to hunt down all those he may have been in contact with after the man became Goma's first confirmed Ebola case on Sunday. He then left Butembo on a bus, and arrived at a health center Sunday showing symptoms of Ebola, the health ministry said.
Other times the violence against health teams has come from residents who do not want their loved ones taken to treatment centers or buried in accordance with guidelines aimed at reducing Ebola transmission.
Congo will not permit the use of further experimental vaccines as it combats an Ebola outbreak because doing so risked "confusing the population", the government said.
Health workers dressed in Ebola protective suits are seen as they prepare an ebola preparedness facility at the Bwera general hospital near the border with the Democratic Republic of Congo in Bwera, Uganda, June 12, 2019.
According to the latest health ministry figures issued on Saturday, 1,655 people have died from the haemorrhagic virus since August 1 previous year, when the disease broke out in North Kivu and spread to neighbouring Ituri.
The Goma patient was described as a pastor who had been on a trip to another town, Butembo, one of the towns hardest hit by the outbreak.
Speaking at a United Nations meeting in Geneva on the outbreak, Congo's minister of health, Dr. Oly Ilunga, called the spread of Ebola to Goma "a warning". An epidemic between 2013 and 2016 killed more than 11,300 people in West Africa.