One man, Vasco Pedro da Gama, had already adopted the girl
.The name of his partner,Junior de Carvalho,was then added to the birth certificate.
Gay women have been granted adoption rights twice before,but this is the first time they have been given to men.
Correspondents say the ruling will not necessarily apply outside Sao Paulo.
But it is part of a wider relaxation of the traditionally strict laws on homosexual rights in Brazil, they say.
The couple's lawyer said that they hoped the case would now make it harder for judges to deny adoption to gay men in the future.
The girl, Theodora, had been living with her adoptive parents since last December, at which point Mr da Gama took the legal steps to adopt her as a single parent.
The two men had been in a relationship for the last 14 years and started thinking about adopting back in 1998, Brazil's Globo newspaper reports.
"If they had tried to adopt as a couple, probably Theodora would not be with them now," the lawyer added.
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