Foden has tested positive for COVID-19, which rules him out of the game.
Tomori and Guehi are suffering from minor injuries at present.
All three will be absent for the Hungary game on Saturday, while Foden will not play on Tuesday against Germany either.
Southgate told reporters: "Phil Foden unfortunately has tested positive for Covid so he's had to leave.
"Hopefully he'll be able to meet up when we come back from Germany."
He added: "Fikayo and Marc Guehi both arrived with injuries but they're progressing well.
"They won't be involved in tomorrow's game but there's a chance of involvement against Germany."