Every player in the Premier League had been issued with a Kick It Out T-shirt to be worn during pre-match warm-ups to show support for the campaign to drive racism from the sport.
But Ferdinand infuriated Ferguson by failing to wear his ahead of Saturday's 4-2 win over Stoke at Old Trafford.
Ferdinand is thought to have been protesting at what he believes to be the relatively weak punishment given to John Terry after the Chelsea defender was only handed a four-match ban despite being found guilty by the Football Association of racially abusing the United star's brother Anton during a match against QPR last year.
The 33-year-old's snub was especially annoying for Ferguson as the United manager, reacting to Reading striker Jason Roberts' revelation that he wouldn't support Kick It Out, had insisted on Friday that all his players would wear the T-shirts.
"I'm very disappointed, he has let us down," Ferguson said after the Stoke game.
"I said yesterday that the players would be wearing it in support of the Professional Footballers Association and that every player should adhere to it. And he goes and lets us down.
"It is embarrassing for me. He will be dealt with, no doubt about that."