United advanced to the next stage of the competition after a Wayne Rooney goal gave them a 1-0 win in their third-round replay at Old Trafford on Wednesday.
Ferguson was just as pleased with the clean sheet kept by Jones and Smalling as he was with the win.
"Absolutely brilliant, the two of them, absolutely marvellous," ESPN quotes Ferguson as saying. "I couldn't be more pleased.
"They have been injured for a while so they needed games and today is going to help them.
"We have several other players who needed a game, Nani and Rooney and Anderson and [Alexander] Buttner, so we have six players who have had a run out."
United will host Fulham in the fourth round of the cup later this month.