Several fans made their feelings known when Fernandez, who has previously made clear his desire to leave Chelsea, came on in the 62nd minute to replace Reece James.
But other supporters gave their backing to the 25-year-old Fernandez, who told the Blues in May he wanted to leave.
Chelsea placed a reported asking price of £120 million on the Argentina international but no bids have yet been received during the summer transfer window.
Fernandez scored Argentina's equaliser in their World Cup semi-final win over England in July before being sent off in the South Americans' defeat by Spain in the final.
Record signing Morgan Rogers scored on his first Stamford Bridge appearance, tapping in the rebound after Joao Pedro's header was saved.
Brazilian Pedro ensured victory for new manager Xabi Alonso in the team's final match before their Premier League opener away to local rivals Fulham, scoring a double to take his pre-season total to eight goals, after Jon Aramburu had equalised for the La Liga side.