Kimmel referred to Hannity as the "chief propaganda guy for Trump's legal team", and noted, "If this is the biggest witch hunt in history, the broomstick is getting pretty full".
The disclosure came as a NY judge disappointed a lawyer for Trump by letting prosecutors proceed with the cataloguing of evidence including multiple electronic devices that were seized in raids while a system is set up to ensure that records protected by attorney-client privilege aren't disclosed to investigators.
But it was the revelation of Cohen's legal relationship with Hannity, who has frequently assailed the investigation into Cohen on the air, that sent shockwaves through the NY courtroom and Washington.
Late night talk show hosts had a field day with Fox News' Sean Hannity being outed as Donald Trump's personal lawyer Michael Cohen's secret third client. Cohen only has two other clients, and all he does is pay off mistresses.
But Judge Wood made one of the lawyers identify Mr Hannity on Monday.
"Following the raid of Mr. Cohen's office and residences, there has been a deluge of press", Cohen's lawyers wrote.
The search sought information on a variety of matters, including a $130,000 payment made to porn star Stormy Daniels, who alleges she had sex with a married Trump in 2006.
But prosecutors said Trump had no more rights under the law than anyone else if his lawyer committed a crime.
He complained that Cohen won't disclose the identity of one of them described as a "publicly prominent individual".
The contract in the confidential settlement between Broidy and Bechard included the same aliases - "David Dennison" and "Peggy Peterson" - that were used in a 2016 contract between Trump and Daniels, according to a person familiar with the deal.
The vocal Trump supporter had never mentioned his involvement with Cohen and last week called the Federal Bureau of Investigation raid an "all-hands-on-deck effort to totally malign and, if possible, impeach the president of the United States".
Daniels, wearing a pink skirt and black heels, stumbled and nearly fell on the wet sidewalk outside the courthouse among a throng of reporters and camera crews.
A recent Trump fundraising email praised Mrs. Trump, with the president calling her "my rock and foundation".
Cohen is "radioactive", said Michael Avenatti, Clifford's lawyer. "Michael never represented me in any matter".
Failing that, they want the court to appoint an independent official known as a special master, a role typically filled by a lawyer, to go through the records and decide what prosecutors can see. The government says it should do the vetting. Her lawyer says she'll be in the courtroom Monday.
"I think it's a huge minefield for Donald Trump and the Trump Organization", said trial attorney Joseph Cammarata, who represented Paula Jones in her sexual harassment suit against President Bill Clinton. "He's not under investigation by anyone", Carlson said.
The submission in Manhattan federal court came prior to a hearing scheduled for the afternoon. "It nearly goes without saying, unfortunately, that none of Mr. Cohen's clients want to be associated with the government raid on his home and law office, or want to be affiliated in any way with the proceedings here and the attendant media coverage".
She argued in Sunday's court filing that a Chinese wall in the prosecutor's office was not enough in the "highly politicised, even fevered, atmosphere" around the probe.
Prosecutors filed papers last week in court revealing that Cohen is under criminal investigation. He has denied wrongdoing.
In a hearing that began Friday, Cohen is seeking to keep federal authorities from reviewing files seized from his homes and officers in an April 9 raid by investigators.