Ferguson accused the experienced centre back of "embarrassing" him by declining to wear a T-shirt in support of the "Kick It Out" anti-discrimination campaign, having told the media his whole squad would don the tops before the Premier League match against Stoke on Saturday.
However, Ferguson backed down Monday, saying "I've spoken to Rio. I think there was a communication problem. He felt I should have spoken to him on Friday and I obviously didn't anticipate that he'd have a problem wearing the shirt.
"As the manager of a club, you lay down policy and you don't want to see it ignored," Ferguson added. "That's where my anger came from on Saturday. But we've resolved the situation, there's no lingering problems and we move on."
Ferdinand was one of many Premier League players to boycott the Kick It Out action this weekend, as a protest against a perceived lack of strong action taken by organizations in recent high-profile racism cases.
The Football Association, which partly funds the Kick It Out campaign, punished John Terry with a four-match ban and fine after finding the Chelsea defender guilty of racially abusing Anton Ferdinand — Rio's younger brother — during a Premier League game last October.
Many believe that sanction, together with Liverpool striker Luis Suarez's eight-match ban for repeatedly racially abusing United defender Patrice Evra in another on-field incident late last year, was too lenient.
"My advice to him (Ferdinand) was that I always feel a union is stronger than an individual," Ferguson said. "It's important he airs his grievances to the right people, to the PFA (Professional Footballers' Association) or the FA."
Ferguson said Ferdinand will not play against Braga in Tuesday's Champions League match at Old Trafford — but stressed it had nothing to do with their dispute over the weekend.
"We have a (Premier League) game on Sunday against Chelsea and it's a big one for us," Ferguson said, "so I'm leaving a couple of players out (Ferdinand and Evra)."
Chelsea and United are the top two teams in the league after eight games.Suggest a correction