The 35-year-old British actor was also going to appear in a cameo in Shazam! but talks broke down due to scheduling conflicts.
Henry first donned the famous blue suit for Man of Steel in 2013, then starred in Batman vs Superman and finally in last year's Justice League.
According to the Hollywood Reporter the main reason that Warner are "dumping" him is because they want to shift their focus to a Supergirl movie, featuring a teenage heroine.
A studio source said that Warner aren't planning another Superman film for "at least several years".
The source said: "There's a recognition that some parts of the previous movies didn't work.
"Superman is like James Bond, and after a certain run you have to look at new actors."
Henry is due to star in Netflix's The Witcher.
The news comes as it is "not expected" that Ben Affleck will reprise his role as Batman – which would confirm the big "shake up".
Meanwhile he recently had to apologise for controversial comments he made regarding the #MeToo movement.
In an interview with GQ Australia, he said: "There's something wonderful about a man chasing a woman.
"There's a traditional approach to that, which is nice.
I think a woman should be wooed and chased, but maybe I'm old-fashioned for thinking that."
He continued: "It's very difficult to do that if there are certain rules in place," Cavill said.
"Because then it's like: 'Well, I don't want to go up and talk to her, because I'm going to be called a rapist or something: "It's very difficult to do that if there are certain rules in place.
Afterwards twitter users called him an "idiot" and one said: "The whole Me Too movement has him scared someone may call him a rapist??
"Just don’t rape anyone."
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