According to Ortin, Gravity & Strings (Chapter 2), we define
$$\dfrac{\delta S}{\delta \phi} \equiv \dfrac{\partial \mathcal{L}}{\partial \phi} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi)}\bigg)$$
Now, as you can easily see,
$$\delta S = \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi} \delta \phi - \dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi)} \delta (\partial_\mu \phi)\bigg) $$
$$= \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi)}\bigg)\bigg) \delta \phi $$
$$=\displaystyle\int d^4x \dfrac{\delta S}{\delta \phi} \delta \phi$$
Edit From this answer, I realize that we don't really need to define an explicit $\dfrac{\delta S}{\delta \phi}$. Rather, we can derive it from the definition of $S$ as it should be the case. Based on the answer linked above, I derive here $\dfrac{\delta S}{\delta \phi}$ in the simplest manner apparent to me. The key is to realize that there is an implicit label associated with $\phi$ which decides what $\phi$ we are talking about - the label is the coordinates $x$.
$$S=\displaystyle\int d^4x \mathcal{L}(\phi(x), \partial_\mu \phi(x)) $$
$$\delta S = \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi (x)} \delta \phi(x) - \dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi(x))} \delta (\partial_\mu \phi(x))\bigg) $$
$$= \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi(x)} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi(x))}\bigg)\bigg) \delta \phi(x) $$
Now, since $x$ is already used in the integration and it runs over all of spacetime, we should use a different variable for coordinate label when we want to define $\dfrac{\delta S}{\delta \phi}$ which is the variation of action with respect to variation in the field at any point in spacetime. Let's use $y$ to denote coordinates of this point where we vary the field and notice the variation in action.
$$\dfrac{\delta S}{\delta \phi} = \dfrac{\delta S}{\delta \phi (y)}$$
$$= \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi(x)} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi(x))}\bigg)\bigg) \dfrac{\delta \phi(x)}{\delta \phi(y)} $$
$$= \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi(x)} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi(x))}\bigg)\bigg) \delta (x -y) $$
$$=\dfrac{\partial \mathcal{L}}{\partial \phi(y)} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi(y))}\bigg)$$
So, $$\dfrac{\delta S}{\delta \phi(y)} = \dfrac{\partial \mathcal{L}}{\partial \phi} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi)}\bigg)$$
And, thus, $$\delta S = \displaystyle\int d^4x \bigg(\dfrac{\partial \mathcal{L}}{\partial \phi(x)} - \partial_\mu \bigg(\dfrac{\partial \mathcal{L}}{\partial(\partial_\mu\phi(x))}\bigg)\bigg) \delta \phi(x) $$
$$=\displaystyle\int d^4x \dfrac{\delta S}{\delta \phi(x)} \delta \phi(x)$$
Or, concisely, ${\delta S} = \displaystyle \int d^4x \dfrac{\delta S}{\delta \phi} \delta \phi$.