Andreas Pereira had Fulham ahead before City fought back to lead 3-1 before Rodrigo Muniz struck on 88 minutes.
"We have to be really unhappy with the result,” Silva said. “That’s the first thing and it’s a feeling that we all share in our dressing room.
“Of course, looking at the performance and the way the players stuck with the plan, they executed it really well and performance-wise it was a very good one.
“Looking at the chances that we did create throughout the game and comparing with City, we deserved more. But that’s football.
“It’s a process for the next time we have these types of chances to be able to score more and get a different result, but coming here to the Etihad, scoring twice and probably having four more clear chances to score is not easy to achieve and we did it.”
Silva said of his tactics: “We defended a little bit deeper than we normally like to. That was the plan. Even if you don’t have that plan, City have the capacity to push you back and we did.
“We changed the position of Alex (Iwobi) and Adama (Traoré) because we wanted to explore some things in the way they set up when they’re in attack.
Adama Traoré comes close to scoring
“We were always able to make some dangerous counter-attacks and create something in those moments.”
He added, “To see City finish with three central defenders with five at the back shows that we were creating problems for them, not just in transition.
“It gives us courage. We know what we are capable of doing, and it gives us the confidence to keep going in the direction that we want to go in, and to stick with our philosophy as a team.”