The Spaniard was the difference with a second-half salvo, although the dogged visitors saw James McArthur's header incorrectly ruled out before the Ivorian settled the game
The Spain midfielder struck twice in the second half on his 200th appearance for the club at the Etihad Stadium on Saturday, as the champions stretched their winning run to eight games in all competitions.
City had been toothless in the first half, with James Milner employed in an unfamiliar advance role in the absence of all of the club's recognised strikers due to injury.
They raised their game after the break, though, and Silva delivered the end product they had previously been lacking with two goals in the space of 12 minutes, before Yaya Toure added a third goal to cap another impressive display.
|VIEW FROM THE EITHAD STADIUM
|By Tom Maston
In the end a routine afternoon for Manchester City, though for 45 minutes it looked as if their lack of a striker was going to see them frustrated in front of their own fans.
David Silva provided the key to unlocking the Crystal Palace defence, and though he needed a deflection to open the scoring, his knowledge of playing in a system without an out-and-out frontman was plain for all to see. Without Sergio Aguero, his role in the side becomes even greater, and on this evidence he is more than ready to carry that burden.
For Palace's part, they battled bravely, but once Yannick Bolasie was shackelled they had very little to offer in the final third. Neil Warnock will no doubt be looking for a striker once the transfer window opens in 12 days.
Palace were unfortunate to have a James McArthur goal disallowed for offside after Silva's second goal and Neil Warnock's team have now won just one of their last 11 games.
Pellegrini made six changes to the side that won at Leicester City last weekend, with Milner among the players to come in, while Fraizer Campbell replaced the injured Marouane Chamakh in the Palace starting line-up and Jason Puncheon was preferred to Wilfried Zaha.
Warnock said his Palace side had nothing to fear at the Etihad Stadium and they made a positive start as City struggled to get going.
Yannick Bolasie proved a real threat early on and Joe Hart did well to palm away the winger's cross as the onrushing McArthur was poised to finish from close range.
Mile Jedinak ought to have headed home an inviting corner, before Campbell spurned a great chance to open the scoring when Bolasie headed the ball on and the former Manchester United striker failed to hit the target with an acrobatic overhead kick.
City started to get into their stride with some slick passing and movement, but Silva was unable to make Julian Speroni work after Samir Nasri had burst into the penalty area and cut the ball back to the Spain midfielder.
Bolasie shot into the side-netting 10 minutes before the break as City continued to look vulnerable at the back.
Pablo Zabaleta then came agonisingly close to putting the home side in front when Toure picked him out with a sublime pass and the marauding defender scooped the ball over Speroni, but his effort was just wide.
It was a frustrating first half for the champions, but they were in front four minutes after the break courtesy of a strike from Silva.
Zabaleta was the architect, with the right-back again surging forward and unselfishly cutting the ball back for Silva, whose shot hit Scott Dann and looped into the far corner of the net.
Palace were struggling to live with City's passing and movement and Silva doubled their lead 61 minutes in, sweeping the ball home first time after Aleksandar Kolarov had picked him out with a fine cross.
The visitors had the ball in the back of the net after 66 minutes, but McArthur was wrongly adjudged to be offside after he headed home a fine cross from the impressive Bolasie.
Toure added to Palace's misery with nine minutes remaining when he fired a powerful left-footed shot past Speroni after receiving a fine pass from Milner following a swift break, as City marched on in ominous fashion.