Magpies boss Steve Bruce opted to recall record signing Joelinton to lead the attack in place of Andy Carroll, while the Saints were unchanged from the side which defeated Norwich City 2-1 last time out.
A quiet opening to the game saw both sides take a cautious approach, before Shane Long fired an effort wide with ten minutes on the clock.
Soon after Allan Saint-Maximin beat a couple of defenders, but his attempted cutback to Miguel Almiron was cut out by the alert James Ward-Prowse.
Goalkeeper Martin Dubravka then came to the rescue for the hosts as he twice denied Nathan Redmond, first blocking an effort when the Saints forward sprinted clear and then repeating the trick from the resulting corner.
On the half-hour mark Alex McCarthy kept out a Ciaran Clark header from a Jonjo Shelvey cross and right on half-time the Saints keeper collected a Fernandez header from another Shelvey delivery.
It was the visitors who made the perfect start to the second half, breaking the deadlock as striker Danny Ings found the net for a fifth consecutive match, latching on to a long ball forward from Jack Stephens to slot his finish past the exposed Dubravka.
The hosts responded by sending on Carroll for Joelinton and he made an almost immediate impact, as his ball back across the face of goal was headed home for the equaliser by the in-form Shelvey.
The Saints almost retook the lead as a Long header was somehow kept out by team-mate Ryan Bertrand, but it was the hosts who eventually snatched a late winner.
McCarthy kept out a drive from sub Sean Longstaff, but Fernandez pounced on the loose ball to power the ball home from close range.