For $n\le 3$, $H_1=1$ and the result has to be checked by hand (easy since $A_2$ is trivial and $A_3$ is cyclic fo order 3). Now assume $n\ge 4$.
The set $C=\{H_1,\dots,H_n\}$ is a single $G$-conjugacy class of subgroups of $A_n$. Hence if $\phi(H_1)=H_i$, then $\phi(C)=C$. The set of $\phi$ such that $\phi(C)=C$ form a subgroup $I_n$ of $\mathrm{Aut}(A_n)$, containing automorphisms induced by elements of $S_n$.
In particular, for $\phi\in I_n$ there is a permutation $s=s(\phi)$ of $\{1,\dots,n\}$ such that $\phi(H_j)=H_{s(j)}$ for all $j$. Then $\phi\mapsto s(\phi)$ is a homomorphism $I_n\mapsto S_n$. If $\phi\in S_n$ then $s(\phi)=\phi$. Hence to show that $I_n=S_n$ it is enough to show that any $\psi$ in the kernel of $s$ is trivial.
By assumption, $\psi(H_j)=H_j$ for all $j$ and let us show $\psi$ is the identity. In particular, $\psi$ preserves the intersections of any $n-3$ of the $H_j$; thus it maps any 3-cycle to either itself or its inverse. Since all cyclic subgroups generated by 3-cycles are conjugate (because $A_n$ acts transitively on 3-element subsets), if $\psi$ is not the identity, then $\psi$ maps all 3-cycles to their inverse. Now (using the right action, so reading permutations from the left to compute compositions), but this yields a contradiction since it would imply
$$(134)=\psi((143))=\psi((123)(243))=\psi((123))\psi((243))=(321)(342)=(142).$$