Ferguson said on Friday his players would wear the shirts and condemned Jason Roberts, who also refused to wear a 'Kick It Out' shirt prior to Reading's defeat at Liverpool.
Sir Alex Ferguson: "I am disappointed. I said (on Friday) that the players would be wearing it in support of the PFA and that every player should adhere to it.
"And he goes and lets us down. We will deal with it, don't worry.
"Everyone should be united, with all the players in the country wearing the Kick it Out warm-up tops.
"I don't know what point he (Roberts) is trying to make.
"I don't know if he is trying to put himself on a different pedestal from everyone.
"But he really should be supporting all the rest of the players who are doing it."
Ferdinand was protesting at what he perceive to be a lack of action by the 'Kick It Out' organisation in combating racism in football.
At Old Trafford and prior to United's game with Stoke, which they won 4-2, all of Ferdinand's outfield team-mates wore the black 'one game, one community' T-shirts as agreed but the former West Ham man sported a bright red United tracksuit top.
Ferdinand eventually took his training top off to reveal he was wearing a United training shirt, with the DHL sponsors logo.
It represents an obvious snub to the anti-racism message, and directly contradicted Ferguson's stance on the matter yesterday when the United boss was asked what he thought of Roberts' protest.
Stoke boss Tony Pulis backed the right of players to decide whether or not they wanted to wear the Kick It Out shirts.
Tony Pulis: "They are given the opportunity and chance to decide.
"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.
"You can do what you want here. You have the chance to stand up and say you don't want to do it.
"This is a great country. It is multi-cultural. It is the best country in the world. They might have a gripe. Maybe rightly so, especially when you see incidents like the one in Serbia.
"I have never - and no club I have managed - have ever worried about anything like that. Black, white, Catholic, Protestant, you treat people as human beings. There is good and bad in religion and colour. You have to be straight down the middle and treat everyone the same."
BUT I ASK YOU - IF A WHITE PLAYER HAD REFUSED TO WEAR THE SHIRT WOULD HE BE CALLED RACIST?