The concept of absolute time was perhaps more of a postulate, rather than an axiom.
If Newton's physics were based on any axioms, it would have to be the principle of relativity, which is perhaps the most profound concept, fundamental to his laws of motion. This principle was first stated by Galileo$^1$. It states that the laws of physics should be the same in all inertial reference frames.
To this principle, Newton added his laws of motion, universal gravitation, and an assertion of an absolute time. He stated
"Absolute, true and mathematical time, of itself, and from its own nature flows equably without regard to anything external, and by another name is called duration: relative, apparent and common time, is some sensible and external (whether accurate or unequable) measure of duration by the means of motion, which is commonly used instead of true time.
So it is perhaps more accurate to not think of this absolute time as being based on an axiom, but rather a postulate, based on his (Newton's) understandings of space and time and other scientists understandings during that era.
$^1$ Newton's laws are invariant under Galilean transformations, described by the equations (for motion along the x-axis) $$x'=x-vt$$ $$y'=y$$ $$z'=z$$ $$\boxed{ t'=t }$$ Note that it becomes apparent that both Galileo and Newton (and others in that era) thought of time as absolute, encompassed in this last equation.