The Chelsea midfielder had long been suspected as the culprit in 2004 after Manchester United had beaten Arsenal 2-0 to end their 49-game unbeaten Premier League run and he has confessed on Sky One's A League Of Their Own.
On the upcoming episode, host James Corden asks 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?"
"Yes," replied Fabregas.
"All of a sudden, I heard noises (from the tunnel) 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 confirmed the pizza hit Ferguson in the face and added: "I apologise Sir Alex, really didn't mean to do that!"
The game itself was given extra spice due to Keown's treatment of Ruud van Nistelrooy in the same fixture a year earlier, after the United striker had missed a penalty.
Arsenal were furious at Gary and Phil Neville for 'kicking' Jose Antonio Reyes, as well as Van Nistelrooy raking his studs down Ashley Cole's shin, and Ferdinand bundling over Freddie Ljungberg when clean through on goal.
Their sense of injustice grew when Wayne Rooney threw himself over Campbell's outstretched leg to win a penalty that turned the game in United's favour.