The ruling came after Rutherford failed to send son Hermes, 8, and daughter Helena, 6, back to their father Daniel Giersch after they spent the summer in New York with the former "Gossip Girl" star.
"From the beginning I have said I will fight for my children," she told ABC News on Monday.
“We are pleased that the American judicial system has prevailed," Giersch's attorney Fahi Takesh Hallin told ABC News in a statement. "Daniel's request to exclude the press today from the courtroom was granted, to protect the children's privacy. In addition, his stance of promoting Kelly's time with the children has not changed."
The case involving the children, who are scheduled to leave the country today, was brought to the New York court when the judge ruled against their mother. Giersch's mother was also there to greet the children.
Rutherford was supposed to send the children back on Friday, but released a statement over the weekend, writing, "I have decided that I cannot lawfully send my children away from the United States to live in a foreign country."
Rutherford's lengthy custody battle has been ongoing since 2012, when a California judge sent the children to live in France with Rutherford's ex-husband Giersch, whose U.S. visa had been revoked.
The 46-year-old actress has been trying to bring the children back to the U.S. for years, but neither California nor New York court claimed to have jurisdiction in that case.
"It puts me as a parent in an odd place if no one is taking jurisdiction," she told ABC News earlier this week. "How do you put your kids on a plane not knowing what is going to happen?"
Giersch's legal team fired back over the weekend after Rutherford released her statement. They sent the actress a letter in which they demanded that Rutherford send the children back to Monaco immediately, followed by a filing in New York County Supreme Court.
Dan Abrams, chief legal analyst for ABC News, said Monday that he thinks what Rutherford did was a "risky move," but he believes the U.S. State Department has "to get involved now."
"I called for them to get involved a while ago when [the kids] were in Monaco, saying they should bring the kids back," he said. "I think they are going to have to get involved, I think they are going to have to make an incredibly hard decision."
The next court date for Rutherford and Giersch is Sept. 3 in Monaco, where the two will work out custodial decision making and more.