The court Thursday granted a request by Sean Goldman's Brazilian relatives that the child remain in Brazil while it considers whether to hear testimony from him.
The decision came one day after a federal appeals court ruled that Sean must be handed over to his father, David Goldman, at the U.S. consulate in Rio de Janeiro, by Friday.
The high court decision Thursday came as David Goldman visited Rio, hoping to see the child, who has dual citizenship. Goldman later told CNN in an interview from Rio that he was disappointed in the latest ruling.
News reports say that because the court will soon go into recess, the case is likely to be delayed until February.
Goldman has been fighting for custody since 2004, when Goldman's then-wife, Bruna Bianchi, took the boy to Brazil for what she said was a vacation in her native country.
Bianchi divorced the boy's father in Brazil and married a prominent lawyer, but died in childbirth last year. The stepfather refuses to return Sean to his biological father.
The case reached the highest levels of the U.S. government earlier this year, during a private meeting at the White House in March between President Barack Obama and his Brazilian counterpart, Luiz Inacio Lula da Silva.
Secretary of State Hillary Clinton has also lobbied for the boy's return to the United States.
A congressman from David Goldman's home state of New Jersey, Republican Representative Chris Smith, also called for the suspension of Brazil's trade preferences until the international custody battle is resolved.
Smith traveled to Brazil with Goldman Thursday and voiced disappointment in the latest decision as well. But Smith told CNN he hoped the matter might be resolved in the coming days.
Some information for this report was provided by AFP, AP and Reuters.