The Red Devils progressed to the quarter-finals thanks to second-half goals from Nani and Javier Hernandez before Jobi McAnuff gave the Royals some late hope.
United were forced to defend stoutly at the death as Reading pushed for an equaliser but Ferguson was thrilled with what his players earlier in the contest.
"It was a good Cup tie. It ended up a really good Cup tie when they got the goal and had a really good go at it,” he said.
"When they got the goal, they then got the ball in the box. We withstood that and I think when you analyse it, we played some great football and should have scored a lot of goals tonight.
"We missed some chances but there were shots saved and I'm really satisfied with the quality of the game.
"A goal can change things and when we got it, we had to defend well. We really should have punished them better, though. At 2-0 you're never comfortable."