Raul Jimenez had Fulham ahead before Danny Ings struck five minutes into injury-time.
Silva later said: “I agree with you, definitely, I think the best team didn't win the game. Very good performance first half, the way we controlled all the first half in our offensive half – I don't remember one shot from West Ham during the first half.
“With players like Kudus, like Bowen and Antonio, the way we controlled well their counter attacks, always trying to play in the way we like to play, controlling the game, being dominant. And we did it.
“Good goal from us, some good chances,” Silva said. “A clear, clear penalty, in my opinion. Incredible how it wasn't a penalty, really difficult to accept. But, even so, very good first half from us, controlling really well.
“Second half, normal reaction from West Ham, first 15 minutes we were a little bit lacking in keeping the ball, we lost many balls and the game was more open – a normal reaction from them.
“After the first 15 minutes of the second half, we started to control the game again. We made some changes and had a good impact on the game, and we started to be in control again.
“We had some shots, some chances second half, and being more clinical and more ruthless we should have killed the game. Even so, I think that was enough, if we kept – like we should – the focus until the last second, that quick throw-in will not happen that punished us.
“We were punished by a moment that we shouldn't, but that's the Premier League, that’s football, and it should make us grow and get more maturity in that type of situation.
“Because, overall, we have to take many positives from the game, from the performance, from our offensive quality. We just need to be more clinical. We should score more goals.”