The Tottenham midfielder did not train with the rest of the England squad in Zelenogorsk on Friday morning, instead continuing recovery work on his own following a thigh injury he sustained in the win over Tunisia.
Alli was not part of the line-up leaked to reporters from a note held by assistant manager Steve Holland this week. It showed a plan to play in a 3-5-2 formation against Panama, with Ruben Loftus-Cheek in place of Alli in midfield.
Marcus Rashford’s name, rather than Raheem Sterling, was also pictured on the note playing in the front two alongside captain Harry Kane.
But Southgate said his notes do not necessarily reflect his choice of his starting team.
England trained behind closed doors on Friday ahead of departing to Nizhny Novgorod on Saturday for the Panama fixture.
Southgate carried out specific work on tactics and shape to prepare for Panama in the session.