Wayne Rooney scored the only goal of the game as United booked a fourth round tie at home to Fulham.
But United did not have it all their own way, and the back-four, with Jones and Smalling at its heart, were given a bruising evening by the visitors, with the likes of Carlton Cole, Ricardo Vaz Te and Kevin Nolan throwing their weight around.
"Jones and Smalling were fantastic, absolutely brilliant," Ferguson told MUTV.
"The two of them were absolutely marvellous and I couldn't be more pleased.
"They have been injured for a while and needed games, so today would only help them.
"We have several other players who needed a game like Nani, Wayne Rooney, Anderson and Nicolas Buttner. So we had six players who had a run-out at a crucial time of the season with Real Madrid coming up and Tottenham on Sunday, so that is good news for us tonight.
"We missed a lot of chances tonight really and we played some good football at times.
"The 15 minute period after half-time was the hardest for us because they just knocked that ball into the box, there were so many bodies all shoving all over the place.
"You really have to handle that and thankfully our two centre-halves were absolutely magnificent in how they dealt with it.
"t was a physical contest to be under and you have to stand up to it."