You just do. If a calculation gives you $\pi$, then you just say it gave you $\pi$. It is a real number and it is as good as any rational in describing any numeric quantity:
$$\text{all physical quantities are described by }\mathbb{REAL}\text{ numbers}.$$
If you must insist on what real numbers are and how we can even conceive of such a number as $\pi$, then you need to look carefully at your definition. As far as physics goes, the definition of the real numbers is
The real number field $\mathbb R$ is the unique ordered field that is Dedekind complete.
This is independent of the multiple possible realizations of this set of axioms from a "more basic" set, and of the multiple representations which you might think of using (such as decimal expansions, continued fractions, Dedekind cuts, equivalent classes of Cauchy sequences, or what-have-you). In describing numeric quantities, we need a structure that allows us to
- add, substract, multiply and divide as usual,
- compare one number to another and always conclude that one is greater than (or equal to) the other, and
- take limits, infima, suprema, derivatives, integrals, and so on.
The definition above embodies all these requirements. Since there is a unique such structure (up to a natural isomorphism), we don't really care what that structure is meant to be.
"But, but, but...", I hear you say, "what about rational approximations? We can never measure an irrational number!" And yes, that is correct. But we can't measure rational numbers, either. Our measurements come with a central value and a finite, nonzero precision: they describe an interval.* If our calculations come out to an irrational number, then all we can say is whether that number is consistent with experiment, and it's exactly the same with a rational number. Say that some calculation predicted a value of 4/3 for some quantity: then, in your own words,
we can approximate $1.33$, $1.3333$, and so forth, increasing the precision, but yet never getting really to $4/3$.
Such is life, and such is the mathematical structure of physics.
*or a probability distribution, if you insist. Same difference, though.