Sterling has struggled for form and fitness this season after moving from Manchester City to Chelsea in a £47.5 million deal last summer, registering nine goals and four assists in 37 appearances across all competitions.
Sources have told ESPN that Sterling, who has 82 caps, remains fully committed to England and his omission in June is a mutual decision based on how best to manage his body ahead of next season.
And after naming his squad at Wembley on Thursday, Southgate told a news conference: "I spoke with him a week or so ago, a general catch-up. He's not happy physically with his condition, he's been carrying a hamstring problem.
"He really wasn't in consideration. We didn't get to the point of whether he should be in or out. He doesn't think he's operating at the level he needs so that was the conversation I had with him."
Eze has scored six goals in eight games for Crystal Palace as they have revived their fortunes under Roy Hodgson. He is yet to make his senior debut but missed out on being part of England's provisional squad for Euro 2020 after suffering an Achilles injury on the eve of the tournament.
"We've liked him for a long time," Southgate said of Eze. "He was very unfortunate just before the Euros. We were going to call him into a prep camp to have a look at him and he got a bad injury. I remember talking to Roy Hodgson about him then and Roy telling me he had picked up an injury in training that day.
"So I think he has finished the season really strongly. He can play in a couple of positions across that attacking line. He is a goal threat. He has got a nice ability, a burst of speed to go past people and to take people out of the game with his dribbling skills. We are looking forward to seeing him a bit closer and everybody I talk to speaks brilliantly about him as a person as well."
Dunk earned his first call-up in four-and-half years after thriving at Brighton and rejoins England's squad along with Aston Villa's Tyrone Mings, whose last cap came in March 2022 against Cote d'Ivoire.
While Nick Pope, Ben Chilwell and Mason Mount miss out through injury, Eze's Palace teammate Sam Johnstone has been included along with Callum Wilson, selected after Ivan Toney was banned for eight months for breaking Football Association rules on betting.
The timing of this international double-header is awkward for Southgate given it comes more than two weeks after the end of the Premier League season with just six days between the Champions League final - contested by Manchester City, who have five played in the England squad, and Inter Milan -- and their first match against Malta.
Asked about the level of motivation for players at the end of a gruelling season which also featured the first-ever winter World Cup, Southgate said: "I don't think the rest of the world will be doing that this summer and we've played North Macedonia twice at home and never beaten them. So, I think we could easily fall into that trap.
"To be a top team, if we want to be European champions, we've got to nail the big games like we did in March and you've got to make sure you nail the more complicated ones because everybody has the view that you've just given.
"It is a good test of commitment, of togetherness. We don't want to let each other down and keep progressing as a team. We have five opportunities to work together before a European Championship if we can qualify and we played so well in March, we need to back it up and make sure we aren't needing to go to North Macedonia at the end of this competition needing a result to get through."
England squad in full: