Anthony Gordon put England ahead in the 55th minute, and they held that advantage for about half an hour.
In the 85th minute, Fernandez produced a superb equaliser after Messi picked him out near the edge of the area.
Lautaro Martinez then secured the win in stoppage time with a header from Messi’s cross.
From Gordon’s goal to Argentina’s leveller, England had just 12% possession, leaving them defending deep for much of the second half.
It became a contest between Argentina’s relentless attack and England’s resilient defence, which survived several close calls.
Argentina persisted, with Messi exploiting gaps in England’s structure and individual tendencies to drive the comeback.
After some early success against Messi, Anderson’s proactive style lost effectiveness as Messi adapted to his opponent on the fly.
Messi even turned Anderson’s aggression against him, lingering on the ball to draw the 23-year-old out before slipping passes around the corner into the space he had vacated.