Kannappan Sampath's suggestion can be completed as follows.
Let $f$ be an automorphism of $S_n$ with the property that it maps all transpositions to transpositions. So $f(1k)=(a_kb_k)$ for all $k=2,3,\ldots,n$, where $a_k\neq b_k$ are elements of the set $\{1,2,\ldots,n\}$. As the permutations $(12)$ and $(13)$ don't commute, their images $(a_2b_2)$ and $(a_3b_3)$ don't commute either. This means that the intersection $\{a_3,b_3\}\cap\{a_2,b_2\}$ is a singleton. Without loss of generality we can assume that $a_2=a_3=a$.
Next I claim that for all $k>3$ we also have $a\in\{a_k,b_k\}$. Assume contrariwise that for some $k>3$ we have $a_k\neq a\neq b_k$. Because $(1k)$ does not commute with $(12)$, we must have $b_2\in\{a_k,b_k\}$. Similarly, because $(1k)$ does not commute with $(13)$ either, we must also have $b_3\in\{a_k,b_k\}$, so $(a_kb_k)=(b_2b_3)$. But this is a contradiction, because then
$$
f(23)=f((13)(12)(13))=(ab_3)(ab_2)(ab_3)=(b_2b_3)=f(1k)
$$
violating the fact that $f$ is injective.
Thus all the transpositions $(a_kb_k)$ move the element $a$, and w.l.o.g. we can assume that $a_k=a$ for all $k$. All the integers $b_k\neq a$, and they must also be distinct, so the mapping $\sigma: 1\mapsto a, k\mapsto b_k$ is in $S_n$. We have shown that $f$ agrees with the inner automorphism $x\mapsto \sigma x\sigma^{-1}$ on all the $(n-1)$ generators $x=(1k),k=2,3,\ldots,n,$ of the group $S_n$, so the claim follows.