With Jonny Evans struggling with a hamstring injury and Nemanja Vidic and Rio Ferdinand rested after the win over Liverpool on Sunday, the youngsters started a game together for the first time since the 3-1 win over Sunderland on December 15.
The match saw several players, including the pair, come into the side after spells out and although he rued profligacy up the other end, Sir Alex was impressed with his side’s defence.
Speaking to MUTV, he said: "Jones and Smalling were fantastic, absolutely brilliant. 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 Alex 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.
"It was a physical contest to be under and you have to stand up to it."