An automorphism of $S_3$, say $\varphi$, is equivalent to a faithful action of $S_3$ on the set $X:=\{1,2,3\}$. The orbit equations $3=1+1+1$ and $3=1+2$ are ruled out, because they would both imply $\operatorname{ker}\varphi=\bigcap_{i\in X}\operatorname{Stab}(i)\ne\{()\}$. Therefore, the only option left is this action to be also transitive. To sum up, this action has stabilizers which:
- trivially intersect;
- are conjugate in $S_3$.
Can I use 1 and 2 to prove that $\varphi$ is inner?
Apparently, an answer is desired. The answer is certainly 'no', because everything written in the question is also true for $S_6$, where not every automorphism is inner (and other permutation groups as well). Thus the two properties cannot be used to prove that every automorphism is inner.
This was why all of the comments are talking about $S_6$ (or $M_{12}$, which also has an outer automorphism).
More prosaic than the outer automorphism of $S_6$, the group $A_3$ also satisfies the conditions, and obviously has an outer automorphism.