Fulham were knocked out of the FA Cup as Sean Longstaff and Dan Burn scored the goals to send Newcastle through.
Newcastle, who last played on January 13 and are without a league win in four, looked fresh as they inflicted more cup misery on Fulham, ending their hopes of silverware following their Carabao Cup semi-final defeat to Liverpool earlier this week.
The west Londoners were sloppy in possession and after Marek Rodak bailed his team-mates out with a quick-thinking stop to deny Kieran Trippier's cross-shot, Anthony Gordon's long-range effort missed the target, whistling past the Fulham goalkeeper's left-hand post.
Rodrigo Muniz was given a rare start and the Brazil forward was taking his opportunity, forcing a fingertip save from Martin Dubravka before his turn of pace saw Fabian Schar give away a yellow card on the break after 21 minutes.
Fulham lacked cohesion after manager Silva made seven changes from the XI that played in Wednesday's Carabao Cup exit.
A great chance went begging for Newcastle when Alexander Isak rounded the keeper but failed to pull the trigger in time as the ball trickled out for a goal-kick.
But Newcastle breached Fulham's defence as the hosts' frailties continued into the 39th minute.
Trippier tested the waters with another inswinging cross which seemed routine for Fulham to deal with.
Kenny Tete and Bobby De Cordova-Reid ran into each other instead of clearing their lines before the ball fell to Longstaff, who powered home from inside the area.
Silva turned to the bench in the form of the experienced Willian and the Brazilian swung the momentum in the Cottagers' favour.
After the winger's long-range goal was chalked off for offside, he enjoyed neat touches and exchanges around the Newcastle area as Silva's side searched for an equaliser.
But it was the Magpies who punished the home side after they failed to clear their lines once again in the 61st minute.
Trippier's corner found Sven Botman, whose header had too much power for Rodak keep hold of the ball.
The Cottagers' back-up keeper parried the ball into the path of Burn, who finished first-time from inside the six-yard area.
