The World Health Organisation said the toddler had travelled hundreds of kilometres by bus from Guinea through Mali showing symptoms of the disease.
More than 40 people known to have come into contact with her have been quarantined.
The girl was being treated in the western town of Kayes, after arriving at a hospital on Wednesday.
The child had travelled more than 1,000 km (600 miles) from Guinea through the capital, Bamako, to Kayes.
“The child’s symptomatic state during the bus journey is especially concerning, as it presented multiple opportunities for exposures, including high-risk exposures, involving many people,” the WHO said.
The girl’s mother died in Guinea a few weeks ago and the child was then brought by relatives to Mali.
Guinea, Liberia and Sierra Leone have seen most of the 4,800 Ebola deaths.
In the US, the governors of the states of New York and New Jersey have ordered a mandatory 21-day quarantine period for all doctors and other travellers who have had contact with Ebola victims in West Africa.
Anyone arriving from affected West African countries without having had confirmed contact with Ebola victims will be subject to monitoring by public health officials.
The moves go beyond anything so far announced at a national level by the Obama administration and come after a doctor, Craig Spencer, was diagnosed with Ebola following his return to New York from Guinea.
People in the city have expressed concern that Dr Spencer used public transport and restaurants before being diagnosed.
At the scene: Alou Diawara, BBC Afrique, Bamako
People are afraid in Mali’s capital, Bamako, but life is carrying on as normal. A few people have stopped shaking hands but physically greeting people is an important part of life in Mali and for most this has not changed.
Some hotels have placed bottles of anti-bacterial gels at their entrances but for ordinary Malians, gel remains too expensive. The government has been running public information broadcasts telling people to wash their hands with soap. But though soap is not expensive, most still wash their hands with water alone.
Many Malians have friends and family in Guinea and several buses and taxis travel between the two countries each day.
With the support of the WHO, Mali’s health system has been preparing for an outbreak of Ebola for several months. But there is a culture here of visiting people when they are sick to wish them a speedy recovery.
This will have to change if Ebola becomes more widespread.
Mali has now become the sixth West African country to be affected by the outbreak, although Senegal and Nigeria have since been declared virus-free by the WHO.
The WHO has three experts in Mali evaluating its ability to cope with Ebola and will send at least four more over the next few days, spokeswoman Fadela Chaib said.
With porous borders, countries neighbouring Guinea, Sierra Leone and Liberia are on high alert for possible imported cases of the virus, says BBC Africa health correspondent Anne Soy.
The BBC’s Gabriel Gatehouse travels with an ambulance worker in Liberia
The World Health Organization (WHO) has meanwhile announced that hundreds of thousands of vaccine doses should be available in the first half of 2015.
WHO Assistant Director Dr Marie-Paule Kieny told a news conference in Geneva that five more vaccines would be in the clinical trial stage in January. Two are already being tested on humans.
Dr Marie Paule Kieny, WHO: “Pharmaceutical companies committed to ramping up production”
“The pharmaceutical companies developing these vaccines, as well as the ones which are a little bit further along the development path, are committing to ramping up the production capacity to millions of doses to be available in 2015 with hundreds of thousands ready in the first half of next year,” she said.
Vaccine trials in the worst-affected countries could begin in December, Dr Kieny said.
In the US, two nurses infected with Ebola while caring for dying Dallas patient Thomas Duncan have been declared free of the virus.
One of them, Nina Pham, 26, had a meeting with President Barack Obama at the White House, hours after being discharged.
“I feel fortunate and blessed to be standing here today,” she said. “I am on my way back to recovery.”
The other nurse, Amber Vinson, has also been declared virus-free, but she will remain in treatment in Atlanta until further notice.
Nina Pham met President Obama in the Oval OfficeNina Pham met President Obama in the Oval Office
Thomas Duncan died earlier this month and it is still unclear how the nurses contracted the virus while wearing protective clothing.
The news of the two nurses’ recoveries comes a day after a new US infection, the first in New York.
Craig Spencer, 33, began to feel tired on Tuesday and developed a fever and diarrhoea on Thursday. He had recently returned from Guinea where he had been working for medical charity, Medecins Sans Frontieres.
Dr Spencer is being kept in isolation at New York’s Bellevue Hospital.
Ebola virus disease (EVD)
How Ebola survivors’ blood is saving lives
Symptoms include high fever, bleeding and central nervous system damage
Spread by body fluids, such as blood and saliva
Fatality rate can reach 90% – but current outbreak has mortality rate of about 70%
No proven vaccine or cure
Fruit bats, a delicacy for some West Africans, are considered to be virus’s natural host