The Republic of Ireland international defender picked up an injury following United's 1-0 away victory at Huddersfield and will be unavailable to face the Cottagers at St. James' Park.
Along with injuries to Jonjo Shelvey and Karl Darlow, Benítez confirmed that United midfielder Ki Sung-yeung will report for international duty after their clash with Fulham, as the 29-year-old competes in the Asia Cup for South Korea during January.
However, Benítez - who welcomes DeAndre Yedlin back from a one-match suspension - was able to reveal some positive news about Federico Fernández, after the Argentine defender missed the clash with the Terriers after limping off against Wolves two weeks ago.
"More or less, we are fine," said Benítez. "We need to check on the progress of Shelvey but he is doing well. We have lost Clark, who had a problem with his ankle after the game (against Huddersfield).
"Fede (Fernández) is fine as well as the rest of the players. (Florian) Lejeune has been training so, to be fair, we have Clark, Shelvey and Karl Darlow ruled out.
"Ki will play the game, hopefully, but after he will go because the manager wants him in Abu Dhabi on the 26th (December) at the training camp.
"He was playing well for us. With Shelvey injured, he was a very good option and hopefully, he will be available sooner rather than later. He gave us composure on the ball but we will just have to manage without him and try to do well."
Newcastle's meeting with Fulham is likely to see ex-striker Aleksandar Mitrovic makes a return to St. James' Park for the first time since departing from Tyneside this summer.
Despite insisting that the Serbian forward does not have a point to prove against the Magpies, Benítez remains focused on guiding United towards a strong finish in the top flight rather than on their former striker.
"He is playing well, scoring goals for them and working really hard so I think he will be happy at the moment," added Benítez.
"Obviously, he will like to score as many goals as he can but I don't feel needs to prove anything because he's a good player. I wish him all the best after the game.
"He will give everything on the pitch so, hopefully, we can keep him quiet. I don't care if he scores if we can score three goals and we win the game.
"My main priority is to make sure the team are in a good position in the table, which I'm happy with at the moment."
