This is obviously a typo: $GL_2(\mathbb Z^3)$ and $GL_2(\mathbb Z^2)$ are infinite, while a finite set like $\mathbb Z_3^2$ only has finitely many bijections from itself to itself.
What is meant is that $\operatorname{Aut}(\mathbb Z_3^2) \cong GL_2(\mathbb Z_3)$. This is just the usual statement from linear algebra that automorphisms of a vector space can be identified with invertible matrices, after a choice of basis. Here the vector space is $\mathbb Z_3^2$ over the field $\mathbb Z_3$.
The only thing you have to think about is that indeed every group automorphism of $\mathbb Z_3^2$ is also a $\mathbb Z_3$-vector space automorphism.