The Hornets led 2-0 against the Toffee’s after quick second-half goals from Richarlison and Christian Kabasele but let their lead slip after goals from Oumar Niasse and Dominic Calvert-Lewin gave David Unsworth’s team a foothold back into the game.
A stoppage-time penalty from Leighton Baines gave the Blues a 3-2 lead but Silva’s side had their chance to level from the penalty spot in the 99th minute of stoppage time but former Everton midfielder Tom Cleverley stepped up and missed after Jordan Pickford had fouled Richarlison.
Speaking to the media after the game, the Portuguese boss said: “It’s a really disappointing afternoon, for us, for our fans as well.
“We did everything well until 2-1. We could play again the same way, we controlled until that moment - the 2-1 - controlled all the match. Even after going up 2-0 we had our opponents under control.
"We gave the Everton players one chance and they started to believe again at 2-1.”
Zonal marking or man to man?
The Portuguese boss was unhappy when quizzed about his side’s use of zonal marking on the corner from which Calvert-Lewin levelled the game for the hosts.
"I respect the opinion, but forget it," Silva said. "We need to do it differently, but Everton did man-to-man and it didn’t work.
"The goal we conceded against Chelsea was a fantastic goal. I understand we need to do things differently, but everything started when we lost the ball and permit the opponent to attack the ball.
Defending his stance, the 40-year-old added: ”You need to work hard. We scored goals from set-pieces and we need to be different in our position."
Everton job links
The Watford boss has been linked with the managerial role at Goodison Park in recent weeks but refused to be drawn into talking about the possibility of leaving Watford before the end of the season.
“We need to talk about the match,” Silva briefly commented before returning to speaking about his side’s disappointing afternoon on Merseyside.
“Like you believe and you understand, it’s a really disappointing afternoon for us, for me, for our players.
“I prefer to talk even after the 3-2. We believed again when we made the change and put Okaka on the pitch, we started to play with heart and in our style of play.”