The boy, now aged four, was conceived through artificial insemination of one of the women in Belgium.
Under French law that procedure is not explicitly open to lesbian couples. The judge said the law had been violated.
France legalised gay marriage nearly a year ago. The Versailles judge's ruling was "homophobic", said ADFH, a group representing homosexual parents.
ADFH said French law had failed to protect the rights of the child.
A lesbian rights activist, Nathalie Allain-Djerrah of Enfants d'Arc-en-ciel (Rainbow Children), said the ruling "shows in a blatant and violent way how inequality persists between the children of homosexual parents and those of heterosexual parents".
According to the French newspaper Le Figaro, in similar cases French judges have allowed lesbian couples to adopt infants since gay marriage was legalised.
France's same-sex marriage law also legalised gay adoption. Opponents staged huge rallies against it but President Francois Hollande signed the "Taubira" bill into law after months of heated debate.
Gay rights groups in France have voiced anger after a judge prevented a French lesbian couple from adopting an infant.