Silva opened the scoring just five minutes into the match with a fabulous goal unleashing a terrific shot into the bottom left corner after a Sergio Aguero pass.
Pep Guardiola's men made it two-nil in the 27th minute, with Silva turning provider for City top scorer Aguero to score with a delightful chipped finish for a well deserved two-goal cushion.
Despite dominating from start to finish, City failed to add more goals with Kyle Walker coming closet to adding a third one with his shot smashing straight onto the right post.
The defeat means Fulham have now lost five of their last five Premier League matches.
Liverpool, who host Tottenham on Sunday, have a chance of reclaiming top spot with a win.