Hull manager Phil Brown had accused Spaniard Fabregas of spitting at the feet of assistant manager Brian Horton after the final whistle in the quarter-final.
"I was there and I witnessed it, he spat at my assistant manager down the tunnel," Brown said at a post-match news conference after William Gallas's controversial late header knocked his side out.
Brown added: "He spat at his feet."
"I categorically deny that I spat at anybody after the match," Fabregas, who did not play in the match because of injury, said in a statement on the Arsenal website (http://www.arsenal.com).
"I have never done this in my whole career on the pitch, so why would I do it when I am not even playing?
"I can understand the frustration of losing a game to a dubious goal, that has happened to me many times in my career as well. But this is not the fault of me or any of the Arsenal players."