Players across England donned the T-shirts during their warm-up routines for league matches as part of a two-week campaign by Kick It Out, an anti-discrimination body that has been raising awareness for issues such as racism since the 1990s.
Ferdinand, however, didn't wear the shirt before United's 4-2 win over Stoke, in protest at Kick It Out's perceived lack of action during recent high-profile racism cases. Ferguson had indicated Friday that the centre back would not boycott the campaign.
"At the press conference yesterday, I spoke to the press about it," Ferguson said. "It is embarrassing for me. He will be dealt with, no doubt about that."
Ferguson added in an interview with United's in-house television channel that Ferdinand's action "lets us down."
"We did that in support of the Professional Footballers Association and every player in the country should have adhered to that," Ferguson said.
Chelsea defender John Terry was recently banned for four matches for racially abusing Ferdinand's brother, Anton, during a league game.
In another case, Liverpool striker Luis Suarez was given an eight-game ban around the turn of the year for repeatedly racially insulting United left back Patrice Evra.
Ferdinand wasn't the only player to refuse to wear the Kick It Out T-shirts on Saturday.
Reading striker Jason Roberts went through with his threat to boycott the campaign — but received support from his manager.
"Jason has had a very strong view of it and I respect Jason's view," Reading manager Brian McDermott said. "It was important to him what he did today. I 100 per cent back him."
Stoke manager Tony Pulis took the same view as McDermott.
"They are given the opportunity and chance to decide," he said. "Let me say this about this country — people have the right to say yes or no. In a lot of countries you haven't the right."
Chelsea and Manchester City players didn't wear the anti-racism T-shirts before their games on Saturday as they intend to do so before matches next weekend.
The two-week Kick It Out action started on Thursday and ends on Oct. 29.