Miller and the 9-month-old boy's mother, former Marine Sara McKenna, cemented the temporary pact in family court in New York City on Monday. It's in place until at least a March 31 court date.
The case became a cause for women's rights advocates after a judge castigated McKenna for moving while pregnant to New York. She's studying at Columbia University.
The boy, who Miller calls Nathaniel in honor of his late younger brother, will spend time with his mother while she pursues her studies.
Case referee Fiordaliza Rodriguez of the Manhattan Family Court approved the agreement, issuing a temporary order after a short conference in her courtroom.
'I'm happy to see that both parties are working this out,' Rodriguez said, according to the New York Daily News.
The child was not present Monday at the courthouse.