We have that the electric field from a "point charge" $q$ located at the origin is
$$\vec E=\frac{q}{4\pi \epsilon_0}\frac{\vec r}{|\vec r|^3} \tag 1$$
Clearly from $(1)$, we have $\nabla \cdot \vec E=0$ for $\vec r\ne 0$. We note that the divergence is undefined (using classical analysis) at the origin.
Now, let $V$ be any region, whose "outer boundary" contains the origin, that excludes the "small" spherical region $0<\epsilon <r$ (i.e., $V$ has a hole to exclude the origin). Denote the "outer boundary" of $V$ to be $S$ and the boundary of the "small" spherical region to be $S_{\delta}$. Clearly, we have from the Divergence Theorem
$$\begin{align}
\int_V \nabla\cdot \vec E\,dV&=\oint_{S} \vec E\cdot \hat n\,dS-\oint_{S_{\delta}} \vec E\cdot \hat n\,dS\\\\
&=0 \tag 2
\end{align}$$
since $\nabla \cdot \vec E=0$ throughout $V$. Equation $(2)$ implies that
$$\oint_{S} \vec E\cdot \hat n\,dS=\oint_{S_{\delta}} \vec E\cdot \hat n\,dS \tag 3$$
for any $S$ surrounding the origin. We can evaluate the integral on the right-hand side of $(3)$ using $(1)$. Proceeding we have
$$\begin{align}
\oint_{S_{\epsilon}} \vec E\cdot \hat n\,dS &=\int_0^{2\pi}\int_0^\pi \left(\frac{q}{4\pi \epsilon_0} \frac{\hat r}{\delta^2}\right)\,\cdot \hat r \,\delta^2\,d\theta\,d\phi\\\\
&=\frac{q}{\epsilon_0} \tag 4
\end{align}$$
which yields the integral-form of Gauss's Law for a point charge.
NOTE:
Analysis can be facilitated using Generalized Functions as follows. In THIS ANSWER, I discuss regularizing the Electric Field of a point charge to assign meaning to the Dirac Delta for use in the Divergence Theorem. This provides a rigorous way forward where Dirac Delta is interpreted in terms of the limit of the regularized function $\vec \psi$ given by
$$\vec \psi(\vec r;a)=\frac{\vec r}{(r^2+a^2)^{3/2}} \tag 1$$
Taking the divergence of $(1)$ reveals that
$$\nabla \cdot \vec \psi(\vec r; a)=\frac{3a^2}{(r^2+a^2)^{5/2}}$$
Now, in the Aforementioned Answer, I showed that for any sufficiently smooth test function $\phi$, we have that
$$\lim_{a \to 0}\int_V \nabla \cdot \vec \psi(\vec r; a)\phi(\vec r)dV=
\begin{cases}
0&, \text{V does not include the origin}\\\\
4\pi \phi(0)&,\text{V includes the origin}
\end{cases}$$
and it is in this sense that
$$\bbox[5px,border:2px solid #C0A000]{\lim_{a\to 0} \nabla \cdot \vec \psi(\vec r;a)=4\pi \delta(\vec r)}$$
Heuristically, let the volume charge density of a point charge be given by $q\delta (\vec r)$, where $\delta(\vec r)$ is the Dirac Delta. Then, the point-form of Gauss's Law is
$$\nabla \cdot \vec E=\frac{q}{\epsilon_0}\delta (\vec r)$$
and we have from the divergence theorem for Generalized Functions
$$\int_V \nabla \cdot \vec E\,dV=\frac{q}{\epsilon_0}=\oint_S\vec E\cdot \hat n\,dS$$
where $\delta(\vec r)$ interpreted in terms of the limit of the regularized function. And we are done!
Other answers I've posted on the subject of the Dirac Delta are HERE, HERE, and HERE. This latter post provides a good primer on Distributions.