The Blues had to win at the Stadium of Light and hoped other results went their way to stand any chance of qualifying for European football.
But even though Cole Palmer cancelled out a strike from Trai Hume and a Malo Gusto own goal, a turnaround wasn't forthcoming and Calum McFarlane's side had to settle for a disappointing 10th-place finish.
To make matters worse, Fernandez made a gesture to the Chelsea fans at half-time that could be interpreted as a "goodbye".
The Argentine international has been linked with a dream move to Real Madrid, while Manchester City are also in the mix with Enzo Maresca's imminent arrival.
Fernandez has been arguably Chelsea's most important player this term with 15 goals and seven assists in all competitions and Xabi Alonso will want him to stay.