Stones did not feature in Saturday's 2-2 qualifying draw with Scotland.
But the Manchester City player could figure in his familiar centre-back role for Tuesday's friendly against France.
Southgate, who has used the 23-year-old in midfield in training, said: "He has all the attributes and capabilities to play as a holding midfield player."
The former under 21s boss, who also figured as a central defender and midfielder during his England career, added: "I think we want defenders who can bring the ball out and show composure. I think he could do either of those jobs.
"You've asked me if he's an option [in midfield]. I think he is. He's a player who is very comfortable receiving possession.
"He obviously hasn't done that yet, really, so that's a decision we have to make - but do I believe he can play that role? Absolutely."
Stones had a mixed first season at Manchester City following a £47.5m move from Everton last summer, missing the conclusion to the 2016-17 Premier League campaign with a muscular injury.
He was left out of the match at Hampden Park on Saturday as Southgate opted to go for the more physical pairing of Chelsea defender Gary Cahill and Manchester United's Chris Smalling.
Southgate explained: "Really, he didn't start because he hadn't played for seven weeks or maybe a bit more. He'd had an injury and didn't get back into the team at the end.
"Cahill had played in the FA Cup final, Smalling in the Europa League final. That had a bearing on my decision.
"But John has huge potential. He'll be a much better player for his experiences at City this year. Defending is a skill you learn and he'll learn a lot with a coach in Pep Guardiola asking a lot of him with the ball."
England defender John Stones may be used in a holding midfield role as manager Gareth Southgate plots a route to the 2018 World Cup in Russia.