Context: Newton personally believed in the concept of absolute space since it reinforced the idea of an absolute God, but the entire premise was proven false by what we know as 'relativity of motion' which makes use of Newton's laws of motion.
Excerpts from 'A Brief History of Time' by Stephen Hawking:
"... Aristotle believed in a preferred state of rest, which any body would take up if it were not driven by some force or impulse. In particular, he thought that the earth was at rest. But it follows from Newton's laws that there is no unique standard of rest."
"Newton was very worried by this lack of absolute position, or absolute space, as it was called, because it did not accord with his idea of an absolute God. In fact, he refused to accept lack of absolute space, even though it was implied by his laws."
Well, two things. First, this Absolute Space concept was something Newton believed, and even though some people believe his laws of motion disprove Absolute Space, Newton didn't believe his laws contradicted Absolute Space. He definitely didn't think his laws concluded that God can't be real.
But as for your example, the question remains "from where?" Setting two things in motion doesn't resolve the issue that there is an equal and opposite reaction. It just means now there are two of them. And if we assume that the laws of the universe do not apply outside the universe, we must also presume that there is a space outside of the universe with its own properties and its own laws. And then therefore there must be a space where the two spaces intersect so that one might affect the other. At that intersection, the universe where physics apply would be acting on the external-space where physics don't apply. If the universe did not affect the external space, it would violate Newton's laws. If it did, it would violate the laws of the external space.
It's an unresolvable conflict, or at least it was during Newton's time. Today, we understand that Newton's description of physics was accurate on a macro level, roughly describing motion and energy in basic terms. I don't know if Quantum Physics or Astrophysics can resolve the conflict. It's not important to me whether or not it is possible for Absolute Space to exist, nor is it important to disprove the possibility of its existence. But I would say that we should follow the science to explore the universe, wherever that leads us. If that means we shed some previously held beliefs, then that's reality for ya.
It would be comforting to think there exists a divine arbiter and prime creator that wants us to be good and happy, and to imagine we get to hang out with our loved ones when we die. I can understand why so many people want to hold on to those concepts. I just don't think the universe is that small or unimpressive.