The court ruled the child must stay in Brazil while it considers a request that his own testimony be heard in the case, which has dragged on for five years.
The ruling written by Justice Marco Aurelio Mello means the boy will be in Brazil at least until Feb. 1, following the justices' return from a recess, according to a court spokesman who commented on condition of anonymity as he was not authorized to discuss the case.
David Goldman's lawyer Ricardo Zamariola confirmed the ruling means he will be unable to pick up his son Sean at the American Consulate in Rio on Friday, as a federal appeals court had ruled on Wednesday.
"We're studying the decision and we'll decide what to do soon," said Zamariola.
It was not immediately possible to contact Goldman in Rio and Zamariola said he had yet to speak with his client.
"At stake is a fully formed life," Mello wrote in his ruling. "At stake is the right to come and go, the right of opinion, expression and human dignity."
Mello told reporters afterward that the coming ruling will "question the necessity of Sean, the boy, who is almost 10-years-old, to be heard directly by a judge."
Silvana Bianchi, Sean's maternal grandmother, told the privately run Agencia Estado news service she was elated with the decision. According to her, Sean, who has dual citizenship, has said he wants to remain in Brazil.
"His testimony has never been heard," she said. "As a Brazilian citizen, he deserves it. He is a child of nearly 10 and he knows quite well what he wants."
Shortly before the stay was announced, Goldman, dressed in black, stepped off a 12-hour flight from New York into a large scrum of reporters at Rio's international airport.
Facing the crowd of cameras and microphones, he looked blank, uttered a few quiet words and appeared every inch a man exhausted from a flight, the custody fight and the chance that, one more time, a last-minute appeal will keep him from taking his boy back to New Jersey.
"I hope I can go home with my son," Goldman quietly told reporters.
President Barack Obama, the U.S. Congress and Secretary of State Hillary Rodham Clinton have all urged the child's return, and a U.S. congressman traveled to Rio on Thursday to continue lobbying for Sean's return.
In 2004, Goldman's wife, Bruna Bianchi, took Sean to her native Brazil.
Goldman says it was to be a two-week vacation, but she stayed and so did the boy. She eventually obtained a Brazilian divorce from Goldman and remarried.
Goldman was already seeking his son's return under an international treaty that covers cross-border child abductions when his former wife died last year giving birth to a daughter.
U.S. Rep. Chris Smith, who has been supportive of Goldman's fight and is in Brazil with Goldman, said he was deeply disappointed by the Supreme Court's ruling and called on Brazil to send the boy back to the U.S. based on international law.
"We have a reciprocity agreement when it comes to abducted children," he said. "We all have an international obligation to work to get children back to their habitual residence."
Sergio Tostes, attorney for Sean's stepfather Joao Paulo Lins e Silva, said the case should never have reached the political levels that it has.
"This is not a fight between two countries," Tostes said. "This is just the pursuit of the truth and the pursuit of what is in the best interest of the boy."
Before the Supreme Court ruling, Zamariola had warned that additional appeals could block the transfer of Goldman's son and forecast that a final resolution would not come until at least the first half of 2010.
Previous rulings favorable to Goldman have been scuttled by Brazilian courts. Zamariola said he was certain lawyers for Joao Paulo Lins e Silva, the Brazilian stepfather with whom Sean lives, would appeal Wednesday's federal court ruling to surrender the boy.
"It's a mixed bag for David right now," Patrick Braden, an international abduction expert whose daughter Melissa was taken to Japan three and a half years ago, told CBS' "The Early Show". "So he's probably a bit skeptical and excited at the same time. It's an emotional roller coaster."
Goldman and Sean were reunited in February for the first time since his son was taken to Brazil. They have not seen each other since June.