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.
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 has raised it in Congress and is in Brazil with Goldman, said upon landing in Rio that this case fell under international law and that the boy had been illegally taken away from Goldman.
"Child abduction is a serious crime and now for over five years David has been trying to get his son," Smith said. "We hope this is the end game and that he'll be reunited with his only father, and that's David Goldman."
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.
Sergio Tostes, attorney for Sean's stepfather Joao Paulo Lins e Silva, declined to comment.
The boy's maternal grandmother says Sean wants to stay in Rio and had filed the separate petition with the Supreme Court asking that the boy's desires be considered.
The child, who has dual citizenship, has been shielded from speaking directly to the news media.
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.
Associated Press writers Marco Sibaja in Brasilia, Brazil, and AP Television News Producer Flora Charner contributed to this report.