Fernandez came on as a second-half substitute in Xabi Alonso's first match in charge at Stamford Bridge, replacing captain Reece James in the 62nd minute of a 3-1 pre-season win over Real Sociedad.
James handed the armband to his vice-captain before embracing him, but the reception that followed was far from straightforward: sections of the crowd booed as Fernandez's name was read out before kick-off and again as he entered the pitch, while supporters in the Matthew Harding and Shed End responded by chanting his name in support.
The Argentina international has been strongly linked with a move to Manchester City throughout the summer, with Chelsea having set a deadline of 5pm on Friday for City to submit a bid meeting their roughly £120m valuation.
That deadline passed without an official offer, though talks between the two clubs are understood to remain ongoing, complicated by Manchester City's parallel pursuit of Rodri from Barcelona.
Fernandez had been given an extended break following Argentina's run to the World Cup final, where he was sent off in the defeat to Spain having scored the equaliser in the semi-final win over England.
Chelsea's win was secured by two goals from João Pedro and one from record signing Morgan Rogers, who scored on his first appearance at Stamford Bridge, with Jon Aramburu replying for Sociedad.
Fernandez was the first player off the pitch at full-time, leaving down the tunnel without engaging further with supporters, one of whom could be heard shouting for his "head" rather than his name as he departed.
Alonso now has just over a week to finalise his squad before Chelsea's Premier League opener at Fulham on August 24, by which point Fernandez's situation may finally be resolved one way or another.