Baby Angel's mother told the BBC her milk had run dry after being separated from the child for the first five months of her life.
The case shocked the country, and she gained much public support.
The bill of 2 million CFA ($3,630; £2,610) was paid after a campaign was launched on the family's behalf.
President Ali Bongo was among those who contributed towards the bill.
The clinic's director was arrested on Monday on baby-kidnapping charges, but the charges were dropped a day later, reports BBC Afrique's Charles Stephan Mavoungou from the capital, Libreville.
Angel was finally allowed to leave the clinic, which is north of the capital, this week.
The baby's mother, Sonia Okome, told the BBC of her relief, but explained it was bittersweet: "I'm happy to have my baby back. But I'm sorry that I can't breastfeed her because after five months all my milk has gone."
She also complained that the baby had not been given any vaccines.
The bill was for the 35 days Angel spent in an incubator after she was born prematurely.
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