The Toffees were forced to play more than half of the match with 10 men following a controversial red card shown to Phil Jagielka, but they twice took the lead through Richarlison before being pegged back on both occasions.
Silva was unhappy with the decision to send Jagielka off, but believes that his side still deserved to win the game even with their numerical disadvantage.
"I saw fantastic attitude and spirit in our squad. Even with the 10 men we were better. We started to grow during the game," he told BBC Sport.
"Phil Jagielka's red card was a harsh decision. Not only the red card but they scored from the free kick. We changed some things at half time and did very well in the second half. We suffered together and in the end we had the best chances to score.
"If someone had to win, it should be our team. But Wolves played well. We worked together and helped each other."
Jagielka's red card was the 90th Everton have received in the Premier League era - more than any other club.