Since the charges were brought Vaughan lost roles as a television pundit and revealed at the hearing in London that his health and wellbeing had suffered.
Christopher Stoner, KC, told the Cricket Discipline Commission in London: “This is obviously a matter of significant importance to my client. The shape of his life and livelihood are at stake.
“We simply say the evidence does not make up the charge.”
Vaughan is alleged to have told Rafiq, Adil Rashid, Rana Naved-ul-Hasan and Ajmal Shahzad: “There’s too many of you lot, we need to have a word about that.”
Stoner accused the ECB of backtracking due to a discrepancy concerning the second half of the comment, as Rafiq also recalled it was: “We need to do something about it.”
ECB lawyer Jane Mulcahy, KC, admitted: “It’s a bit messy, I see that.”
But she was reiterated that the key words “you lot” is what the disciplinary panel should focus on.
Vaughan, who attended the hearing on Friday, maintains he has no recollection of making the comment, and his lawyer cited what he called “the frailties of human recollection” of an incident that took place almost 14 years ago.
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“Mr Rafiq says he has a clear recollection, but not of the exact words,” said Stoner.
“He said it made him feel sick and angry but he didn’t speak about it for 11 years.
“We say it’s inherently improbable he would not have spoken about it to someone.”
Stoner also criticised what he called the “wholly inadequate” investigation by the ECB, notably its failure to contact other players involved in the match, the umpires or a Sky camera operator whose footage formed part of the evidence.
“Due process matters and in our submission it was sent on holiday by the ECB,” he added.
Vaughan’s 32-page closing written submission, accompanied by a 22-page storyboard of the Sky footage, stated: “As this hearing closes, now some 5,006 days after the words were alleged to have been spoken, the burden of proving that the words were said, which is so plainly on the ECB, has simply not been discharged.
“The overall reliability, sufficiency and weight of the evidence, in the context of what is a very serious matter, is such that it is simply not possible for the panel to determine that it is more probable than not that the alleged words were spoken by Mr Vaughan.”
Stoner said it was “inherently improbable” Vaughan would have made such a comment within earshot of a camera operator with a microphone, “when as far as he knew it was being broadcast to the public”.
Earlier, ECB lawyer Mulcahy had asserted that it was “inherently probable” that Vaughan made the comment.
She said the fact Vaughan shook hands with “only the Asian players” was telling.
“This action clearly signifies that he identifies the four cricketers as a distinct group, consistent with the words ‘you lot’,” she said.
The ECB’s closing submission read: “Michael Vaughan cannot refute the words because he cannot remember saying them. Instead, he asserts he would not have said those words.”
The alleged comment, the ECB said, was made only a year before Vaughan sent some tweets which the 48-year-old later agreed were “completely unacceptable”.
“Those tweets were ostensibly light-hearted but in reality were offensive, as he also accepted,” added the submission.
“His comment to the players on June 22, 2009, was in the same vein.”
Mulcahy concluded: “The CDC should find that Michael Vaughan said the words alleged; that the words were racist and/or discriminatory, and that the words may be prejudicial to the interests of cricket or may bring Michael Vaughan or the game of cricket into disrepute.
“That being the case, Michael Vaughan is in breach of directive 3.3.”
The cases of former Yorkshire head coach Andrew Gale and ex-bowling coach Richard Pyrah – who along with Matthew Hoggard, Tim Bresnan and John Blain did not attend the hearing to defend themselves – were also heard. Both deny using racist and/or discriminatory language.
A seventh player, Gary Ballance, admitted a charge while Yorkshire have admitted four charges, including one that it “failed to address systemic use of racist and/or discriminatory language over a prolonged period”.
The hearing is scheduled to continue in private on Wednesday and Thursday.
CDC chair Tim O’Gorman wrapped up the public section of the proceedings, saying: “These are judgments that need careful consideration. These are decisions that will be given in writing, and we hope to have them by the end of the month.
“However, I hope you understand the panel has considerable professional commitments.”