Which noun was referred to after comma?

Your question isn't easy to answer, as you have written it.

But the Ptolemaic astronomy put the Earth at the centre of the universe, and assumed that everything else rotated around it.

Copernicus decided that the planets orbited around the Sun, not the Earth.

Here is how I would interpret your sentence:

Ptolemaic astronomy considered Earth the center of the universe. What the sentence is stating is that Copernicus determined that the sun was the center of the solar system, and therefore Earth was not the center (or the most important) planet in the solar system, and that Earth was one of several planets orbiting the sun.

It is appositive to "Copernicus". It says that Copernicus was moving the sun, etc. Given the context, it also communicates that that this was the result of offering his replacement. So it can be seen as modifying "offered"; it's saying "Copernicus had offered his replacement for the old Ptolemaic astronomy, and in offering his replacement, he moved the sun". "moving" is not referring to "replacement", as it's characterizing the action (verb) of "offer", not the thing (noun) of "replacement", and it's definitely not referring to "the old Ptolemaic astronomy".