Martin Keown, who had left Arsenal for Leicester in the summer before the match, hinted at the assailant, commented to Sportsmail in 2014: "From what I understand, it was a Spanish fella with great technique. Even when it came to the pizza he had great technique. He threw it like a Frisbee."
And now, while making an appearance on A League of Their Own, the Spanish Chelsea midfielder has confirmed he was the culprit.
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?"
The 30-year-old immediately replied, "yes!", before going into the story - although his mind was probably playing tricks on him regarding Keown: "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 then turns to the camera on the show and adds: "I apologise Sir Alex, really didn't mean to do that".
When asked by Jamie Redknapp where the pizza hit Ferguson, Fabregas then taps the side of his own face.
The game itself was tense as it came a year after the famed Battle of Old Trafford. In that previous encounter, Ruud van Nistelrooy missed a penalty before being aggressively surrounded by Arsenal players, who had kept their dream of an undefeated season alive.
During the match two United players could have been sent off. Van Nistelrooy raked his studs on Cole's ankle before Rio Ferdinand could have been dismissed for denying a clear goalscoring opportunity.
The tension only built after Wayne Rooney was felled in the Arsenal box and referee Mike Riley awarded a penalty, which Van Nistelrooy put away.
A 19-year-old Rooney then sealed the points with a close range strike late on.
The two managers ended up in a huge confrontation after Wenger angrily spoke to Van Nistelrooy at the final whistle.
Soon the players became involved. Cole says some shouted "you cheats" at the United squad. Phil Neville remembers "handbags" between the two sides.
Suddenly, Ferguson had pizza thrown at him. United had provided the away dressing room with food. Cole recalls escaping to the dressing room and everyone on the Arsenal side laughing at the incident.
Fabregas's admission has revealed the truth behind this famous incident, one that has had as much speculation surrounding it as Bigfoot or the Loch Ness monster.