However, she can visit Hermes, 9, and Helena, 6, in either France or Monaco, where they will live with their father, Rutherford's ex-husband Daniel Giersch, the judge ruled.
"The habitual residence of the minor children is fixed at the residence of Giersch," the judge ruled, according to court documents obtained by ABC News.
Rutherford and Giersch will jointly make decisions pertaining to the health and education of their children, the documents added.
A representative for Rutherford and an attorney for Giersch declined to comment to ABC News about the ruling.
Rutherford, 47, and Giersch, 41, have been battling for custody since 2012, when a California judge sent their kids to live with their German-born father in France, as his U.S. visa had been revoked. Later, neither a California nor a New York judge claimed jurisdiction in the case, and in August, after spending the summer with her kids in New York City, Rutherford refused to send them back to Europe.
"It puts me as a parent in an odd place if no one is taking jurisdiction," she told ABC News at the time. "How do you put your kids on a plane not knowing what is going to happen? Clearly this was not thought out in a way."
Manhattan Supreme Court Judge Ellen Gesmer disagreed, and, a few days later, ordered Rutherford to send the children back to Monaco. Rutherford appealed to the U.S. State Department for help, but to no avail.
"It was the most cruel act against a child I have ever witnessed in my entire life and the fact that it happened to American children at the hands of an American judge, in a United States courtroom is just inconceivable," Rutherford wrote in a statement to ABC News at the time. "Knowing she had no authority, Judge Gesmer seized my children and their U.S. passports, and forced them to leave the United States and reside in Monaco, a country where neither they nor I, nor even their father, has citizenship."