Judge Saliann Scarpulla also signed off on an agreement Thursday to close the Trump Foundation and distribute about $1.7 million in remaining funds to other nonprofit groups.
A request for comment was emailed to Trump's lawyer.
New York's attorney general filed a lawsuit last year alleging Trump and his family illegally operated the foundation as an extension of his businesses and his presidential campaign.
Attorney General Letitia James had been seeking about $2.8 million in restitution from the president. Scarpulla cut that amount to $2 million.
Foundation lawyers have previously said the lawsuit is politically motivated.