Alli was doubtful for the fixture in Nizhny Novgorod, and Southgate has now officially ruled the 22-year-old out as the Three Lions seek to claim back-to-back wins in Russia.
"This morning [Alli] followed the exact programme we had planned," the England boss told reporters.
"He started training with the rest of the group and then did some more running on his own, so he's progressing really well.
"We're really pleased with where he is at, but he wouldn't be ready for the game."
Alli is likely to be replaced in the starting XI by Chelsea's Ruben Loftus-Cheek.