If convicted of the most serious charges, Weinstein could still get jail time and faces a maximum sentence of life in prison.
He also claimed a police officer had corruptly attempted to influence the case by keeping a witness from testifying about her misstatements.
The woman told the detective in February that Weinstein had offered them money to flash their breasts during the restaurant encounter.
In a story published by The New Yorker magazine a year ago, Ms Evans alleged the assault happened during a meeting in his office when she was a 21-year-old student.
She says Weinstein forced her into oral sex in 2004.
The count stems from charges brought forth against the disgraced movie producer in May and July by the Manhattan District Attorney's Office. The prosecution assured they are "moving full-steam ahead" on all other counts.
A lawyer for Evans insisted that even though this charge was thrown out, her client's claims are still truthful.
"Going forward, I would like to make one thing clear", Assistant Defense Attorney Joan Illuzzi said in court, "nothing in the disclosure relating to Count Six impacts the strength of the remaining case and the remaining counts in the indictment, all five of them, including predatory sexual assault". "Nor does it reflect on Lucia's consistent allegation that she was sexually assaulted with force by Harvey Weinstein", lawyer Carrie Goldberg said. "It only speaks volumes about the Manhattan DA's office and its mishandling of my client's case".
His lawyer, Benjamin Brafman, said in court that he believes Evans lied to the grand jury about what happened.
Evans claims Weinstein forced himself on her, but the witness says otherwise. Outside court, he suggested that Evans should be prosecuted criminally for perjury.
"This is an attack on the fundamental integrity of the grand jury process".
The Associated Press generally does not identify people who say they are victims of sexual assault unless they consent to being identified publicly, as Evans has.
Brafman identified the detective in the case as Nicholas DiGaudio.
A message left on a phone used by the detective in the past wasn't returned.
There was no immediate response from the New York Police Department.
Evidence has been found, according to the defense, that Evans sent several emails indicating that the sex act was consensual and the two carried on an affair for many years, WCBS 880's Marla Diamond reported.
Weinstein has been accused of misconduct by dozens of women, allegations that torpedoed his career and helped launch the #MeToo movement.
"The evidence shows that the criminal case against him is strong", the statement said.