Fulham won 2-0 via goals from Raul Jimenez and Jay Stansfield.
Silva later said: "It doesn't matter about the individual quality of the players when you make 11 changes - five players made their debut this this evening, plus Josh King in the second half, the number is big, even if you are talking about some of them, experienced Premier League players - they never played together and it's going to take time to gel everything.
"I took the decision because I want all of them to be in the right physical shape. It's not because fatigue is not in the thinking for the next game, it is really because most of them need these types of games to be at same level.
"I think it was a tough game, tough place to come. It was a very good test for us in the middle of the week, away from home. It was our aim to keep a clean sheet, that was important too. They had a lot of corners and crosses, and I think our backline responded well.
"We got the penalty and, of course, a very good assist from Andersen - excellent move from Jay and we scored. 2-0, in that moment we should probably be calmer and keep the ball more to control the game - in some moments was not possible, but we were solid enough to control the intensity of the game and the energy that they play with.
"We are in the next round is the most important thing."