The Brighton forward went up for a high ball with the Argentinian defender, before they clashed heads and both men were down for a period of eight minutes at St James' Park.
Murray appeared to be knocked unconscious when the Toon defender nodded the back of his head.
Seagulls skipper Bruno was the first to the scene and seemed to offer some sort of treatment to Murray as panicking players urged dawdling medical staff to hurry.
When they eventually came on to the pitch, Newcastle's Yshinori Muro even helped run the stretcher on.
Both sets of fans applauded Murray who left St James' Park on a stretcher with an oxygen mask on his face after being seen to by doctors.
He appeared to be taken away in an ambulance, which was waiting near the corner of the St James' Park pitch.
Dutchman Jurgen Locadia came on for Murray after the incident with the Seagulls official Twitter account confirming their "concern" for the player.
Fernandez did not need to be taken off by Rafa Benitez after the incident.
And Brighton took the lead against Newcastle thanks to Biram Kayal's opener.
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