Bosses made the decision after showing the clip to a test audience who found it too shocking.
Writers Paul Wernick and Rhett Reese realised they had overstepped the mark when fans reacted badly.
Rhett revealed: “We shot it and we put it in front of an audience.
“He’s got the crib and he’s standing in the German nursery and he’s leaning over the crib.
“It was cut just because, it was at the very, very end, and it left the audience with this, ‘Ohhh?’
“It’s like, sure, it’s baby Hitler, but it is a baby. It’s kind of weird to watch that”
“It’s like, ‘Sure, it’s baby Hitler, but it is a baby. It’s kind of weird to watch that.’
We are Deadpool but there is a line we can’t cross.”
Paul added: “There’s even a draft of that scene where we back it up even more where he’s standing over baby Hitler and says, ‘God, that is a toughie.’ He finds a Sharpie and draws a moustache on the baby, and says ‘Maximum effort!’”
However, the scene could still appear as an extra on DVD copies.
The sequel, which has received rave reviews, is more violent and has more X-rated jokes than the first.
It tells the story of wisecracking superhero Deadpool who enlists the help of three mutants to save a boy from baddie Cable.
The first movie made more than £555m around the world and the follow-up is forecast to make £250m in the opening weekend alone.
Cineworld has enjoyed a 10% profit surge after a spree of superhero flicks such as Black Panther and Avengers: Infinity War.
And it’s set for another boost with the release of Deadpool 2, Solo: A Star Wars Story and Jurassic World: Fallen Kingdom.