The former president had attempted to sue the paper for its Pulitzer Prize-winning expose articles into his finances but lost his $100 million (£78 million) lawsuit.
Mr Trump had accused the Times of using his estranged niece Mary to hatch "an insidious plot" to obtain the tax records.
However, last year a judge threw out Mr Trump’s claim - saying it "fails as a matter of constitutional law".
The New York Times verdict concludes a bad week for the 77-year-old, whose mother in law Amalija Knavs died on Tuesday. Mr Trump also saw his former cabinet member Chris Christie take a parting pop shot at him when he exited the race for the Republican presidential nomination.
Nonetheless, Mr Trump remains the frontrunner to be the candidate on the ballot sheet for the party come November’s vote - despite facing court indictments.
New York Supreme Court Judge Robert Reed ordered him to pay back $392,638 to the New York Times - to reimburse the newspaper for their legal fees. This was a "a reasonable value for the legal services rendered," he said.
The articles in question date back to 2018 when the Times reported that Mr Trump was involved in "dubious tax schemes".
"Today's decision shows that the state's newly amended anti-SLAPP (strategic lawsuit against public participation) statute can be a powerful force for protecting press freedom," a spokesperson for The New York Times said on Friday.
"The court has sent a message to those who want to misuse the judicial system to try to silence journalists."
A spokesman for Mr Trump told CBS News: "All journalists must be held accountable when they commit civil wrongs.
“The New York Times is no different and its reporters went well beyond the conventional news gathering techniques permitted by the First Amendment."