Silva and Villa are expected to be sold this summer by Valencia.
"We played a game to win and ended a season at home with win. Today we had to discard certain players and play with people who were better prepared mentally and physically to play," said Emery at the final whistle.
"Any coach wants to have his future team set as soon as possible, but it is certain that some issues take time. We are resigned to the departure of important players, but while they're here we will count on them. The summer will be long."