The doctor, whose name has not been released, worked at the Bamako clinic where an Islamic preacher, Oussa Koita, from Guinea was admitted last month.
BBC reports that the preacher was initially diagnosed with a kidney problem and has since died, along with another health worker.
More than 5,400 people have died in those three countries, along with a handful of others in Nigeria, Spain and the US.
According to Mali's government, five people have now been confirmed as having died from Ebola in the country.
It is not clear if this includes Koita, as he was buried before tests were carried out.
A two-year-old girl also died from Ebola in Mali last month in a separate case, which has not led to any further infections.
At least 300 people are currently under surveillance in Mali, the authorities there say.
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