"Unfortunately she died between 4pm and 5pm," a source within Prime Minister Moussa Mara's office said on Friday.
The young girl's death has also reportedly been confirmed by the governor of the western region of Kayes.
The girl had recently returned to Mali from neighbouring Guinea, one of the countries most affected by an epidemic that has killed nearly 4900 people.
According to the BBC, the girl travelled over 1000km from Guinea to Kayes in Mali.
There are concerns for other passengers on the public bus have been exposed to the Ebola virus, as the girl had a bleeding nose on the trip.
Fourty-three people who came into contact with her have isolated for treatment.
The girl's mother had died a few weeks earlier in Guinea, and relatives brought by the girl to Mali.