Fulham had Joachim Andersen sent off, with Jaden Philogene also seeing red for Villa. The visitors won via goals from Morgan Rogers, Ollie Watkins and Issa Diop, who put through his own net. Raul Jimenez had initially put Fulham ahead on five minutes.
Villa goalkeeper Emi Martinez also denied Andreas Pereira from the penalty spot.
Silva said, "We knew from the beginning that they would stop us from the build-up.
"We knew we had to have different ways and need to mix our game up. One of them was to go in-behind and that's what we saw. The goal is a good example of that, but unfortunately they equalised too close to our goal.
"Not the best performance from us. We can talk about the own goal, the set piece goal and missing a penalty, but in terms of performance it wasn't our best."
On the missed penalty, he added: "I felt the team were a bit more nervous and we were not playing at out levels. We tried to adjust things at half-time, but the reality is we concede a goal.
"The red card and the own goal. The moments that have an impact in the game were all against us and all for Villa.
"The reality is in decisive moments they punished us."