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The message shown when X Button is clicked on Y Page, has been changed to “Z”.

There is a page Y.
There is a button X on page Y.
There was a message appears when the button was clicked.
The text of the messaged was changed to text "Z".

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In the sentence

The message shown when X Button is clicked on Y Page, has been changed to “Z”.

the comma separates two incomplete thoughts. Simply removing the comma clears the sentence up.

The message shown when X Button is clicked on Y Page has been changed to “Z”.

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Your sentence is grammatically correct, but uses a lot of passive voice: generally speaking this is a Bad Thing, because it makes the sentence more complicated and it doesn't say who is doing something. Better, therefore, to use the active voice with something something like

When [the user] presses the X button on the Y page, the [device] now shows a message Z.

The items in square brackets were not mentioned in your example so I am guessing what they should be: the reader has to make the same guesses too, and maybe won't make the right guesses. The word now indicates that [somebody] has changed the message: is it important to specify who made the change?

Click here https://owl.english.purdue.edu/owl/resource/539/02/ for more information about passive versus active voice.

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