The incident took place in October 2004 after Arsenal saw their 49-match unbeaten run come to an end at the hands of bitter rivals Manchester United at Old Trafford.
Both sides clashed in the tunnel after the game and the fracas ended when then-United manager Ferguson was hit in the face with a slice of pizza.
Fabregas had often been deemed the culprit, with former Gunners Matin Keown claiming as much, and the Spain international has finally come clean.
Speaking on television show A League of Their Own, host James Corden asked Fabregas: “Tonight, can we finally put the case of the flying pizza to bed once and for all? Were you the culprit that thew the pizza?”
Fabregas, 30, replied: “Yes. [But] Martin Keown is a liar because I saw him in front of me just, like, punching people so he didn't see anything.
“All of a sudden, I heard noises and I thought what's happening? So I go out with my slice of pizza and I saw Sol Campbell, Rio Ferdinand, Martin Keown... everyone pushing each other.
“I was like I want to get in but I don't know how to and I threw... peeew... just threw it. Once I saw it was hitting, like, who it was hitting, which I didn't mean.”
Fabregas added: “I apologise Sir Alex, really didn't mean to do that.”