Moonves kept a relatively low profile in August, but remained in charge of the broadcasting behemoth.
The woman interviewed in the latest story alleges sexual harassment or assault by Mr Moonves between the 1980s and the first decade of this century.
Allegations against the CBS executive include coercing women to perform oral sex, exposing himself, forcibly kissed unwilling participants, and threatening to derail the careers of those who rejected him.
In a second statement after his departure, Moonves said he was "deeply saddened" to be leaving the company and its employees.
In a statement to the magazine, Moonves said the "appalling accusations" are untrue, but he acknowledged consensual relations with three of the women before he started working at CBS. "I can only surmise they are surfacing now for the first time, decades later, as part of a concerted effort by others to destroy my name, my reputation, and my career", he said.
Farrow had a different explanation.
The L.A. Times said CBS' board will wait until the conclusion of an investigation into allegations of misconduct.
Moonves is a major Hollywood figure, and was both "the public face of the company" and "an integral part of daily life at the CBS broadcast network and major assets such as Showtime and the nascent CBS All Access streaming service", according to Joe Adalian's analysis at Vulture. "Time and again, we have developed and executed strategies that capitalize on our unique and advantageous position, and what's most exciting is that we are still in the early innings of that process", Ianniello wrote.
These allegations speak to a culture of toxic complicity at CBS, where the safety of women was continuously ignored to protect the careers of powerful men and the corporation. He could not immediately be reached to comment on Sunday after the latest claims.
"The board will make a determination whether the company has grounds to terminate the employment of Mr. Moonves for cause under his employment agreement within thirty (30) days following completion of the final report of the independent investigators in the current internal investigation, but in no event later than January 31, 2019", the SEC filing stated. Discussions had focused on the size of a severance package, and on whether Moonves would move to a producer role, the Times reported.
In reaction to early reports that Moonves was negotiating an exit package that could be worth north of $100 million, several accusers expressed outrage that the longtime mogul could be so enriched from the scandals.
"For me, it has been another sleepless night thinking about this, the pain that women feel, the courage that it takes for women to come forward and talk about this, and I really didn't know what I was going to say this morning", she continued. As a result of Farrow's article, more women are coming out of the woodwork to share their experiences of harassment, intimidation, and assault at the hands of the executive.