Fix any $s\in S$. Define three sets: $T=\{\,t\mid t,st\in S\,\}$, $T_1=\{\,t\mid t\not\in S\,\}$ and $T_2=\{\,t\mid st\not\in S\,\}$. Then, clearly, $T=G\setminus(T_1\cup T_2)$. Hence
$$|T|=|G|-|T_1|-|T_2|+|T_1\cap T_2|>|G|-\frac{|G|}{4}-\frac{|G|}{4}=\frac{|G|}2$$
Moreover, if $t\in T$ then
$$st=((st)^{-1})^{-1}=\pi(t^{-1}s^{-1})=\pi(t^{-1})\pi(s^{-1})=ts$$
Hence $T\subseteq C_G(s)$. Hence $|C_G(s)|>|G|/2$ and so $C_G(s)=G$ for any $s\in S$, which implies that $S\subseteq Z(G)$. So $|Z(G)|>\frac34|G|>\frac12|G|$ thus $Z(G)=G$