The court ruled that a federal court should decide whether the boy will return to the U.S. or remain with his stepfamily in Brazil.
The boy's Brazilian mother died last year, but she had already remarried and Sean's stepfather and family want the boy to remain with them.
What began as a family dispute has become an international controversy.
President Barack Obama has discussed the custody case with Brazilian President Luiz Inacio Lula da Silva in Washington earlier this year, and U.S. Secretary of State Hillary Rodham Clinton has lobbied for the boy's return to live with father David Goldman, of New Jersey.
But David Goldman's attorney said Wednesday that the federal court in Rio de Janeiro, which previously ruled the boy be returned to the U.S., still must consider another appeal from the boy's stepfamily.
Ricardo Zamariola said, "Sean will not be able to leave immediately because a federal court of appeals in Rio de Janeiro has ordered that the boy remain in Brazil until it rules on an appeal filed by Sean's stepfamily."
Nevertheless David Goldman said he was pleased with the Supreme Court decision.
"I hope it will diminish the time away from my son," he said.
Goldman said that the hearing also made public another issue that he said he had been legally barred from discussion previously.
"The psychological damage that has been inflicted on my son is finally out in the open," he said. "There's no words to describe the anxiety and the pain that I feel from that. Fortunately, it's been exposed."
Goldman's lawyer told the judges about reports by three court-appointed psychologists who found he was suffering.
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