A federal judge on Monday ruled that President Trump’s lawsuit against the Internal Revenue Service was an improper exercise in self-dealing and barred him from claiming that the extraordinary tax protections he received were part of a legitimate settlement agreement.

In the order, the judge, Kathleen M. Williams, also referred the lawyer who brought Mr. Trump’s case against the I.R.S. to the Florida bar for potential disciplinary proceedings. Judge Williams added that she would forward her decision to the New York bar, which is already investigating the acting attorney general, Todd Blanche.

The decision by the Judge Williams did not explicitly kill the deal that Mr. Trump had worked out with his own government to receive what amounted to amnesty from investigations into tax returns that he, his family and their businesses have already filed. But Judge Williams’s scathing ruling exposed the negotiations between Mr. Trump’s personal lawyers and senior officials at the Justice Department he controls for what she says they were: backroom dealings that did not arise from a legitimate legal process.

“The nature of the suit itself and the conduct of the parties and counsel from its filing make plain that this was an attempt to use the court to provide some legitimacy to an agreement to confer immunity to people and entities affiliated with the president and to earmark billions of dollars from American taxpayers to redress grievances not defined in the law,” the judge wrote.

The 56-page decision, issued in Federal District Court in Miami, came two months after the Justice Department released a pair of documents purporting to be formal agreements that settled Mr. Trump’s remarkable suit against the I.R.S. The documents laid out a pair of separate but shocking moves — one granting the president, his family and his businesses wide-ranging immunity from tax inquiries and the other creating a $1.8 billion fund aimed at compensating allies of Mr. Trump who say they were the victims of so-called government weaponization.

After outcry from Republicans on Capitol Hill, the acting attorney general, Todd Blanche, said the Justice Department would not move forward with the fund. But he said that Mr. Trump’s extraordinary protections from I.R.S. scrutiny would remain in place.