Congo's health ministry said the girl, called Benedicte, is the youngest survivor in what is now the world's second-deadliest ever Ebola outbreak.
Figures show the death toll in the African nation has jumped to 289, as neighbouring countries remain on high alert amid fears it could spread.
The ministry tweeted a photo of the infant, swaddled and with her tiny mouth open surrounded by caregivers who watched over her 24 hours a day for weeks.
The baby's mother, who had been struck down with Ebola, died in childbirth, the ministry confirmed.
The infant was discharged from the treatment center in Beni on Wednesday. 'She went home in the arms of her father and her aunt,' the ministry said.
The Democratic Republic of Congo's Ebola outbreak, which began in August, is showing no signs of slowing down.
Experts have reported worryingly high numbers of children with Ebola in this outbreak, accounting for a third of all cases.
And the latest figures show 515 people are feared to have been struck down, of which 467 cases have been confirmed. Data also reveals 255 confirmed deaths.
In video footage shared by UNICEF, Benedicte is shown in an isolated treatment area, specially set-up to deal with the outbreak.
She is cradled in the arms of health workers donning protective gear and by Ebola survivors, called 'nounous,' who can go without certain gear, such as masks.
'This is my first child,' her father, Thomas, said. 'I truly don't want to lose her. She is my hope.'
Children who contract the hemorrhagic fever, responsible for a brutal epidemic in West Africa in 2014, are at greater risk of dying than adults.
Ebola typically infects adults because they are most likely to be exposed to the lethal virus. However, children have been known in some instances to catch the disease when they act as caregivers.
Few cases of Ebola in babies have historically been reported, but experts suspect transmission could happen via breast milk or close contact with infected parents.
So far, more than 400 children have been left orphaned or unaccompanied in this outbreak as patients can spend weeks in treatment centers, UNICEF said.
A kindergarten has opened next to one treatment center in Beni 'to assist the youngest children whose parents are isolated' there, it added.