It was a ferocious start, which saw Kenny Tete pick up a yellow card after just a few minutes for the visitors, before Magpies forward Nick Woltemade hit the left-hand post with a sliced effort inside the six-yard box.
Just 10 minutes into the match, Newcastle were already rampant - seeing Bruno Guimaraes go close from range, before Murphy’s fierce shot from a tight angle was tipped onto the post by Bernd Leno.
Despite the Cottagers finding some composure since the early assault on their goal, an opener for the hosts was still looking inevitable.
And indeed, on 18 minutes, the pressure told - albeit in calamitous nature - when Murphy took advantage of Calvin Bassey dawdling on the ball to steal possession and fire home a low strike which seemed to take Leno off guard, much to his embarrassment.
Fulham responded well to going behind, and with 15 minutes of the half remaining, Sander Berge shot from the edge of the box which Nick Pope parried into the path of Adama Traore, who could only muster a cross-cum-shot across the face of goal.
With five minutes remaining of the half, Newcastle should have doubled their lead when Anthony Gordon played in Murphy, but Leno did well to get a touch on his eventual strike and force the ball out for a corner, which proved to be the last notable effort before half-time.
The visitors needed a bright start to the half and Marco Silva brought on exciting young Brazilian forward, Kevin, tasked with finding an equaliser.
And just 10 minutes after the restart, the new arrival found Raul Jimenez with a cross and, after the Mexico international fired his strike off the crossbar, Cottagers midfielder Sasa Lukic headed in for a well-deserved equaliser.
Magpies manager Eddie Howe responded with a triple attacking substitution in the hope of finding an immediate response, but with 15 minutes remaining of regulation time, it was Fulham who were finding an extra gear and looking the most likely winner.
However, with five minutes remaining, it was the hosts who went closest to a late winner when Joelinton saw his header fly into the side netting, following an excellent cross by Kieran Trippier.
Moments later, Sandro Tonali then saw his effort superbly saved by Leno, and the Magpies sensed a late twist.
The script was set, and Newcastle captain, Bruno Guimaraes, slotted home a parried shot by William Osula which was to prove a 90th-minute winner.
The result sees Newcastle climb to 11th whilst Fulham languish in 16th - just three points off of the relegation zone.
Flashscore Man of the Match: Jacob Murphy (Newcastle United)