According to the report’s sources, he appeared to be on a second call and seemed unaware of what his colleagues had allegedly seen.
In a statement to the website, Mr Toobin said he believed he had not been visible and apologised to family, friends and co-workers for the “embarrassingly stupid mistake”.
A New Yorker spokesperson told the Jewish Chronicle on Thursday: “As a result of our investigation, Jeffrey Toobin is no longer affiliated with the company.”
Mr Toobin, who is also CNN's chief legal analyst, previously served as an assistant US attorney in Brooklyn.
He is the author of nine non-fiction books. His latest, “True Crimes and Misdemeanors: The Investigation of Donald Trump”, was published in August.