The two deaths in Mali have dashed optimism that the country was free of the highly-infectious pathogen and caused alarm in the capital Bamako, where the imam was washed by mourners at a mosque after his death.
It came as the World Health Organization (WHO) announced on Wednesday that the outbreak -- almost entirely confined to west Africa -- had passed a gruesome landmark, with 5,160 deaths from around 14,000 cases since Ebola emerged in Guinea in December.
The WHO and aid organizations have frequently pointed out that the real count of cases and deaths could be much higher.
In Mali, the latest country to see infections, the clinic where the imam died has been quarantined, with around 30 people trapped inside including medical staff, patients and 15 African soldiers from the United Nations mission in Mali.
The nurse who died of Ebola had treated the imam at Bamako's Pasteur clinic.
Teams of investigators are tracing health workers, and scouring the capital and the imam's home district in northeastern Guinea for scores of people who could have been exposed.
The deaths have raised fears of widespread contamination as they were unrelated to Mali's only other confirmed fatality, a two-year-old girl who had also arrived from Guinea in October.
A doctor at the Pasteur clinic is thought to have contracted the virus and is under observation outside the capital, the clinic said.
A friend who visited the imam has also died of probable Ebola, the WHO said.
Mali's health ministry called for calm, as it led a huge cross-border operation to stem the contagion.
The WHO said the 70-year-old cleric, named as Goika Sekou from a village on Guinea's porous border with Mali, fell sick and was transferred via several treatment centres to the Pasteur clinic.
Multiple lab tests were performed, the WHO said, but crucially not for Ebola, and he died of kidney failure on October 27.
He had travelled to Bamako by car with four family members -- all of whom have since got sick or died at home in Guinea.
The imam's body was transported to a mosque in Bamako for a ritual washing ceremony before being returned to Guinea for burial.
Traditional African funeral rites are considered one of the main causes of Ebola spreading, as it is transmitted through bodily fluids and those who have recently died are particularly infectious.
The nurse who died treating Sekou, identified by family as 25-year-old Saliou Diarra, was the first Malian resident to be confirmed as an Ebola victim.
The virus is estimated to have killed around 70 percent of its victims, often shutting down their organs and causing unstoppable bleeding.
Ebola emerged in Guinea in December, spreading to neighbouring Liberia and then Sierra Leone, infecting at least 13,000 people.
Cases are "still skyrocketing" in western Sierra Leone, according to the WHO, although Liberia says it has seen a drop in new cases from a daily peak of more than 500 in September to around 50.
The US military has scaled back plans for its mission in Liberia to fight the Ebola outbreak, and will deploy a maximum of 3,000 troops instead of 4,000, said General Gary Valesky, head of the American military contingent in the country.
But the move did not signal less concern about the threat posed by the epidemic, he told reporters in a telephone conference.
Britain's foreign secretary Philip Hammond announced plans Wednesday for hundreds of Ebola treatment beds in Sierra Leone within weeks, admitting the global response had been too slow as he visited the former colony.
The Ebola outbreak has also hit the world of sport.
Morocco were stripped of the right to host the 2015 Africa Cup of Nations after insisting on a postponement.
Angola had emerged as the frontrunner to replace Morocco as eleventh hour hosts but pulled out of the running on Wednesday.
Organisers the Confederation of African Football are due to announce the replacement hosts in the next few days.
In New Zealand, police on Thursday ruled out the presence of the deadly virus in one of three mystery vials discovered in mailboxes this week.
Tests on the two other vials have not yet been completed.
The vials were contained in suspicious packages sent to the US embassy and parliament buildings in the capital Wellington and to a newspaper office in Auckland.
Meanwhile in the US, nurses demonstrated outside the White House on Wednesday saying they are woefully ill-prepared to handle an Ebola case.
They were among thousands of health care workers taking part in protests in the United States and overseas amid fears the Ebola epidemic might spread beyond west Africa.
Two nurses are among the nine confirmed Ebola cases that have been treated in the United States.
- Serge Daniel