The 3-0 defeat at St James' Park two days earlier had seen an argument between Bowyer and fellow midfielder Dyer rapidly escalate as the former approached the latter and they began to scrap, with punches being thrown.
Players from both sides intervened and the pair were dragged apart before referee Barry Knight showed each the red card.
In the post-match press conference, Bowyer and Dyer, sat either side of boss Graeme Souness, each issued an apology. After the players had departed, Souness said he felt Bowyer was "indefensible", adding: "I think he is guilty, as the pictures show, of throwing more than one punch and he has to accept whatever punishment comes his way."
Newcastle subsequently released a statement on the Monday which said: "Lee Bowyer has been handed an unprecedented fine, severely censured and additionally warned as to his future conduct by Newcastle United following his attack on team mate Kieron Dyer during Saturday's home match with Aston Villa.
"The decision to fine and censure Bowyer was taken after chairman Freddy Shepherd and team manager Graeme Souness interviewed both players at the club's training ground this morning.
"The fine, amounting to six weeks' wages, is the highest fine handed out by the club."
Bowyer's fine was thought to amount to around £200,000.
The statement continued: "In Kieron Dyer's case, in accordance with the disciplinary regulations of the Football Association the club has, on the player's behalf, submitted notice of the player's intention to submit a claim of wrongful dismissal from the field of play. This claim will be submitted by noon tomorrow together with video evidence.
"Both players have had a fair hearing and the club is fully in support of Kieron Dyer's claim to the Football Association."
Bowyer initially faced a four-match ban for what was his second sending-off of the league campaign, and, after he admitted using violent conduct, it was subsequently extended to seven games by the FA. He was also given a £30,000 fine, to add to the fine from Newcastle.
Dyer served a three-match suspension after the FA rejected the club's appeal against his red card.
The following year Bowyer was fined £600 and ordered to pay £1,000 costs after pleading guilty at Newcastle Magistrates Court to using threatening behaviour. He had just moved on to West Ham – where he would again be a team-mate of Dyer, who the club signed in 2007.