Vaughan is accused of telling a group of Yorkshire players of Asian ethnicity, including Rafiq, that there are “too many of your lot” before a County Championship match against Nottinghamshire in 2009.
The former England captain has strongly denied the allegation – which has been backed up by other players including England bowler Adil Rashid – on multiple occasions.
Vaughan was stood down from his BBC radio show amid the allegations and will not be part of the Beeb’s Ashes coverage in Australia due to what they view as a “conflict of interest”.
The First Test begins at the Gabba in Brisbane on December 8.
“While he is involved in a significant story in cricket, for editorial reasons we do not believe that it would be appropriate for Michael Vaughan to have a role in our Ashes team or wider coverage of the sport at the moment,” BBC Sport said in a statement on Wednesday.
“We require our contributors to talk about relevant topics and his involvement in the Yorkshire story represents a conflict of interests.”
Vaughan – who was due to be part of Test Match Special’s coverage in Australia – is still set to cover the Ashes series for Fox Sports, and has a column in the Daily Telegraph.
He posted on Instagram: “Very disappointed not to be commentating for TMS on the Ashes and will miss working with great colleagues & friends, but looking forward to being behind the mic for Fox Cricket in Australia.
“The issues facing cricket are bigger than any individual case and I want to be part of the solution, listening, educating myself and helping to make it a more welcoming sport for all”.