Brighton captain Lewis Dunk is rewarded for his fine season with a first call-up for four-and-a-half years.
Sterling, who has won 82 caps, has endured a difficult first season since joining Chelsea from Manchester City.
A representative for the forward said his absence was part of a mutual decision to allow him to focus on "recuperating his body in preparation for the upcoming season".
England are well on course to qualify for Euro 2024 in Germany after beating Italy and Ukraine in their opening Group C fixtures.
Gareth Southgate's men travel to Malta on June 16 before hosting North Macedonia at Old Trafford three days later.
Eze's performances have caught the eye, with six goals in eight games under Roy Hodgson, who returned to Selhurst Park as coach in March.
Dunk's only previous cap came against the United States in November 2018.
Southgate revealed Sterling's absence was largely down to fitness issues rather than form.
"I spoke with him a week or so ago - a general catch-up," he said.
"He's not happy physically with his condition, having 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 is operating at the level he needs."
The England boss said he was looking forward to working with midfielder Eze.
He said: "We have liked him for a long time. I think he has finished the season really strongly. He can play in a couple of positions across the attacking line.
"He is a goal threat, he's got nice ability and speed to go past people and can take people out of the game with his dribbling skills. We are looking forward to seeing him a bit closer."
England squad
Goalkeepers: Jordan Pickford (Everton), Aaron Ramsdale (Arsenal), Sam Johnstone (Crystal Palace)
Defenders: Harry Maguire, Luke Shaw (both Manchester United), John Stones, Kyle Walker (both Manchester City), Kieran Trippier (Newcastle), Marc Guehi (Crystal Palace), Lewis Dunk (Brighton), Trent Alexander-Arnold (Liverpool), Tyrone Mings (Aston Villa)
Midfielders: Jude Bellingham (Borussia Dortmund/GER), Conor Gallagher (Chelsea), Declan Rice (West Ham), Jordan Henderson (Liverpool), Kalvin Phillips (Manchester City), Eberechi Eze (Crystal Palace)
Forwards: Phil Foden, Jack Grealish (both Manchester City), Harry Kane (Tottenham), Bukayo Saka (Arsenal), Marcus Rashford (Manchester United), James Maddison (Leicester), Callum Wilson (Newcastle)
