The duo both turned in superb performances in the 2-1 Premier League win at Stoke.
Injury has hampered Ferdinand for the last two seasons and Sunday's narrow win was only the third time the duo have played alongside each other in the league all season.
The pair were instrumental in United's hat-trick of league titles between 2007 and 2009 and looked back to their very best on an afternoon which saw them head clear countless crosses, free-kicks and Rory Delap throw-ins as Javier Hernandez's double earned a first away win of the season.
Ferguson may have spent the week persuading Wayne Rooney to stay at the club but is under no illusions as to the importance of a solid back four.
He said: "It doesn't matter when you come here, it is always a difficult time. It is one of the hardest places to come in the league. They are such an enthusiastic and motivated team they make you play all the time.
"Both our central defenders will have sore heads. Rio and Nemanja were fantastic, really fantastic.
"You have to defend well because they get so many set-pieces and throw-ins. They got a lot of free-kicks and you have to defend them well.
"We did defend well and if we can defend like that for the rest of the season we will be back to a real solid determination to deal with all these things which will make some difference to us."
Another member of United's back four was lucky to stay on the pitch and Ferguson explained the bizarre substitution of Gary Neville.
Neville was fortunate not to be shown a second yellow card by referee Andre Marriner when he up-ended Matthew Etherington just before the break.
The former captain surprisingly reappeared with the rest of United's players at the break but was then humiliatingly instantly replaced by Wes Brown before the half could kick-off.
It was a strange way to celebrate Neville's 600th appearance for the club but Ferguson explained that he had wanted to give Brown the first five minutes of the second period to complete his warm-up.
He said: "The referee told Gary Neville one more foul and he was off I understand.
"I just wanted to get Wes Brown a warm-up but when I got back to the dugout Wes said he was ready to go on. I was going to wait but I thought Gary should get some applause from the fans - their fans!"