Coming into the tie having scored a miserly 15 goals in 15 games, Newcastle went behind when Southampton striker Danny Ings held off a defender before shooting across keeper Martin Dubravka for his fifth goal in five league games.
The home team had plenty of possession and threatened repeatedly from the flanks but it took the introduction of substitute Andy Carroll to turn the game in their favour.
More used to attacking crosses than putting them in the box, Carroll lofted the ball in from the wing for Jonjo Shelvey to get up highest to plant the ball in at the far post and even out the scores in the 68th minute.
Roared on by the home crowd, the Magpies went looking for a winner and it came as full time approached when Sean Longstaff's shot from distance was fumbled by Alex McCarthy but Fernandez was on hand to thump the ball into the back of the net.
The win put Newcastle in 10th position in the table on 22 points, while Southampton remain in the relegation zone in 18th spot with 15 points. (Reporting by Philip O'Connor; editing by Clare Fallon)