By symmetry, the electric field along the $z$ axis will have only a $z$ component with
$$E_z(0,0,z)=\left.-\frac{\partial \phi(x,y,z)}{\partial z}\right|_{(0,0,z)}$$
Therefore, we have
$$E_z(0,0,z)=\frac{\sigma z}{\pi \epsilon_0}\int_0^{a/2}\int_0^{a/2}\frac{1}{(x^2+y^2+z^2)^{3/2}}\,dx\,dy$$
Rather than attempt a transformation to cylindrical coordinates, we proceed here with integrating directly in Cartesian coordinates.
We evaluate the inner integral by making the substitution $x=\sqrt{y^2+z^2}\tan \theta$. This yields
$$\begin{align}
\int_0^{a/2}\frac{1}{(x^2+y^2+z^2)^{3/2}}\,dx&=\left.\left(\frac{x}{(y^2+z^2)\sqrt{x^2+y^2+z^2}}\right)\right|_{0}^{a/2}\\\\
&=\frac{a/2}{(y^2+z^2)\sqrt{(a/2)^2+y^2+z^2}}
\end{align}$$
Therefore, we have reduced the expression for the electric field along the $z$ axis to
$$E_z(0,0,z)=\frac{\sigma z}{\pi \epsilon_0}\int_0^{a/2}\frac{a/2}{(y^2+z^2)\sqrt{(a/2)^2+y^2+z^2}}\,dy$$
To evaluate the remaining integral, we make the standard trigonometric substitution $y=\sqrt{(a/2)^2+z^2}\tan(u)$. Then, we have
$$\begin{align}
E_z(0,0,z)&=\frac{\sigma z(a/2)}{\pi \epsilon_0}\int_0^{\arctan\left(\frac{a/2}{\sqrt{(a/2)^2+z^2}}\right)}\,\,\frac{\cos(u)}{z^2+(a/2)^2\sin^2(u)}\,du\\\\
&=\frac{\sigma z(a/2)}{\pi \epsilon_0}\int_0^{(a/2)/\sqrt{(a/2)^2+(a/2)^2+z^2}} \frac{1}{z^2+(a/2)^2v^2}\,dv\\\\
&=\frac{\sigma }{\pi \epsilon_0}\arctan\left(\frac{(a/2)^2}{z\sqrt{2(a/2)^2+z^2}}\right)
\end{align}$$
NOTE 1:
We can recover, of course, the potential along the $z$ axis by integrating the electric field. In this problem, integration by parts facilitates. This is left as an exercise for the reader.
NOTE 2:
As $a\to \infty$, the arctangent goes to $\pi/2\,\text{sgn}(z)$, and we recover the familiar result of the electric field from a uniform surface charge on an infinite surface, namely $\vec E(0,0,0^{\pm})=\pm \hat z\,\frac{\sigma}{2\epsilon_0}$.
NOTE 3:
As $z\to 0^{\pm}$, the arctangent goes to $\pi/2 \,\text{sgn}(z)$ and the electric field is $\vec E(0,0,0^{\pm})=\pm \hat z\,\frac{\sigma}{2\epsilon_0}$
NOTE 4:
As $z\to \pm \infty$, the arctangent goes to $\frac{(a/2)^2}{z^2}\,\text{sgn}(z)$ and the electric field is $\vec E(0,0,z\to \pm \infty)=\pm \hat z\,\frac{\sigma a^2}{4\pi \epsilon_0\,z^2}$, which appears as the field from a point charge $q=\sigma a^2$.