Stones is part of the squad which will travel to Portugal for a training camp this week, before flying to Miami to play friendly games against Ecuador and Honduras.
"John deserves to be involved in the group that are going to Portugal and Miami," Southgate told Everton's official website.
"The last period of the season where he was in the first team at Everton, he was so accomplished.
"He's so comfortable with the ball and so composed in possession of the ball, but he's good with his one-on-one defending, he's been a pleasure to work with and I'm delighted for him."
England will return from Portugal to face Peru in a friendly at Wembley on May 30.