Pakistan's government had appealed to the court on Friday to review its decision to free the British-born Islamist and three others convicted in the case, a day after their acquittal by a panel of three judges.
Pearl's family had also petitioned for the Supreme Court to reverse the acquittal.
In a decision that is expected to draw criticism from the United States, the court recommended that Ahmad Omar Saeed Sheikh be transferred to a government safe house as a stepping stone to his full release after spending 18 years on death row.
Sheikh's father, Ahmad Saeed Sheikh, attended Tuesday's hearing.
His lawyer, Rauf Ahmad Sheikh said there was "no justification" for his client to remain imprisoned after the acquittal.