The Spaniard fired home a rebound after just two minutes and then struck a sublime second in the 69th minute as the champions enjoyed a comfortable win at the Etihad Stadium.
Silva could have completed a hat-trick moments later but shot narrowly wide. City will hope the victory puts pressure back on United ahead of their tricky trip to Tottenham. Roberto Mancini's men looked confident from the outset against a side that had won just two of their previous 14 league games.
They made a blistering start as Edin Dzeko took up an early attack and was allowed to shoot from 25 yards. Mark Schwarzer parried his fierce effort but Fulham had been caught short and Silva followed up to rifle in the rebound.
Fulham were unable to get anything going in response and Gareth Barry took command in midfield. Twice he won possession to set moves in motion that led to chances, the first as he released Silva down the left. The Spaniard curled in a good cross for Dzeko but the Bosnian headed straight at Schwarzer.
Fulham made a positive start to the second half as they created a chance for Steve Sidwell outside the area but he sliced well wide and City upped the tempo.
Carlos Tevez broke towards the box but just as he looked to have found space to shoot Sidwell slid in to eliminate the threat. Tevez then fired over and Pablo Zabaleta raced into the box to win a corner after clashing with Brede Hangeland.
Silva took the set-piece as Zabaleta received treatment and Vincent Kompany leapt highest to head on for Tevez but the Argentinian's attempt on goal three yards out was smothered by Schwarzer.
Zabaleta returned to the field but could not continue much longer and, aside from his outstanding form, left the field amid some concern as City's only fit right-back. City were able to cope without him for the rest of the afternoon and doubled their lead soon after his exit following some brilliant play by Tevez and Silva.
The Spaniard started the move, finding Gael Clichy out wide and the left-back's pass inside was cleverly flicked back into Silva's path by Tevez. Silva then did the rest, running into the area and hitting a delicate left-foot lob over Schwarzer to score off the post.
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