Gary O'Neil has also been added to the injury list with a suspected hamstring pull.
In addition, Southgate will also be without Afonso Alves, Emanuel Pogatetz and Chris Riggott.
There are hopes that Andrew Taylor and David Wheater will be fully fit by the weekend.
Southgate: "How many times have we been talking about injuries to key players at crucial times in games?
"It's incredible the way it has gone on and on. It proves costly at the end of the day.
"The last couple of weeks have not been kind to us in terms of injuries and we just have to battle through it.
"We are still waiting for news of Stewart and of course we have got Gary O'Neil injured as well.
"The only positive news at the moment is that Wheater should be OK. He was out on his legs at the final whistle and suffering from cramp, but his knee problem does not seem to be any worse."