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.
Speaking to United's in-house TV channel MUTV, Ferguson said: "I am disappointed. I said yesterday that the players would be wearing it in support of the PFA and that every player should adhere to it."
He added: "And he goes and lets us down. We will deal with it, don't worry."
Roberts and Ferdinand were protesting at what they perceive to be a lack of action by the 'Kick It Out' organisation in combating racism in football.
After high-profile incidents involving Reds striker Luis Suarez - banned for eight matches - and Chelsea's John Terry - suspended for four games - in the last year, Roberts was particularly unhappy with the latter punishment.
"The four-match ban was, for me, not a heavy enough sanction for what happened," Roberts said in the week. "I'm totally committed to kicking racism out of football but when there's a movement I feel represents the issue in the way that speaks for me and my colleagues, then I will happily support it."
While Ferguson condemned Ferdinand, Reading boss Brian McDermott stood firmly behind Roberts.
"Jason has had a very strong view of it and I respect Jason's view," he told Sky Sports News. "It was important to him what he did today. I 100 per cent back him."
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. It represents an obvious snub to the anti-racism message, and directly contradicted Ferguson's stance on the matter.
Source: PA
Source: PA