The 5-4 vote came in the case of an unidentified woman who has sought for the last eight years to adopt a 12-year-old girl who her partner of more than 20 years had through in vitro fertilization. It was the first time that the court heard a case on same-sex adoptions.
A majority of judges upheld the constitutionality of a law that states a person cannot adopt a single-parent child if the would-be adopter is of the same sex as the child's mother or father without that parent losing their legal rights.
The judges also said a family composed of a mother and father is best for a child's dignity, stability and well-being.
"The state ... has not criminalized their sentimental relationship, but it does not have a constitutional obligation to award this relationship the same rights that other relationships have when it comes to adoption procedures," the majority's opinion said.
The majority also found that so-called second-parent adoptions, in which couples jointly adopt children, do not apply in Puerto Rico. That issue affects the case in question in part, the majority said, because the girl would have to be registered with two mothers and the U.S. territory's laws do not address such a situation.
The judges said it is up to legislators to change adoption laws if they see fit.
"Starting today, the applicant should channel her efforts through the Legislative Assembly," the majority wrote, noting that courts in Nebraska, Ohio, Wisconsin and Connecticut have struck down similar cases.
CABE, an umbrella group that represents more than a dozen local human rights organizations, said the opinion shows the legal and social vulnerabilities of the island's gay and lesbian community.
"This opinion saddens us because we know that today they have emotionally destroyed a Puerto Rican family and left it without legal protections," said spokesman Osvaldo Burgos.
Chief Justice Federico Hernandez Denton dissented from the ruling, calling the law unconstitutional and saying the plaintiff's lawyers proved the proposed adoption would benefit the child. The girl, he noted, "proudly states: 'I have two mothers.'"
"Both (women) have ideal emotional skills, intuition and protective instinct to guarantee the girl's full and healthy development," he wrote. "In addition, tests showed that (the girl) is mentally stable, does exceptionally well in school and gets along very well with children her age."
By not allowing a second parent adoption, the girl does not benefit from the woman's medical insurance or a possible will, and the petitioner would lose custody if the girl's birth mother died or if the couple broke up, he said.
Hernandez began his opinion with a quote from President Barack Obama's inaugural address in January, in which he said that "our journey is not complete until our gay brothers and sisters are treated like anyone else under the law."
The chief justice criticized the judges who upheld the law, saying they interpreted Puerto Rico's constitution in the context of the times in which it was adopted more than 60 years ago, "as if it were an ancient manuscript encapsulated in a crystal urn."
Hernandez also noted that in 1976, Puerto Rico's Supreme Court allowed a single woman to adopt the daughter of her ex-lover without him losing his biological rights.
"While the rest of the world keeps opening its doors to the legitimate complaints of human beings discriminated against for their sexual orientation, the majority of this court refuses to declare the law in question as unconstitutional," he said.
The court's opinion comes as Puerto Rican legislators prepare to debate several bills that would extend more rights to gays and lesbians, setting off a heated debate in recent weeks.
On Monday, tens of thousands of people of different religious backgrounds marched to the island's seaside capitol to defend the traditional views of marriage and family involving a mother and a father. Several legislators joined the march, with protesters carrying signs that read, "Puerto Rico belongs to Jesus" and "Puerto Rico Stands Up in Defense of Family."
Human rights activists criticized Wednesday's court ruling. Among the critics was Puerto Rican pop star Ricky Martin, who tweeted his displeasure: "How sad. I see this as turning your back on childhood. So many orphans wanting the warmth of 1home."
William Ramirez, director of the American Civil Liberties Union in Puerto Rico, said he didn't think the court's opinion would set a strict precedent for future cases involving same-sex adoptions.
"We have a court that is pretty much divided on the issue," Ramirez said. "With a new set of facts in a future case, there's room to believe this could change."