Given two vectors $s$ and $S$, there are multiple rotations taking $s$ to $S$. given $R$ such that $Rs=S$, we can choose any rotation $R'$ such that $R's=s$ and $RR'$ will also satisfy $(RR')s=S$.
More information is needed to uniquely determine the original rotation.
Edit: determining $R$ from two pairs of vectors
First, note that the cross product $\times$ is preserved up to sign by rotations:
$$
R(u\times v)=\begin{cases}
(Ru)\times(Rv) & R\text{ is a proper rotation} \\
-(Ru)\times(Rv) & R\text{ is an improper rotation}
\end{cases}
$$
Suppose we have vectors $s,t,S,T$ with $s,t$ linearly independent and we know that $Rs=S$ and $Rt=T$ for some rotation $R$. Since $s,t$ are linearly independent, $s,t,s\times t$ forms a basis for $\mathbb{R}^3$. The same is true of $S,T,S\times T$, since rotations preserve liner independence. Thus we have
$$
R[s,t,s\times t]=[S,T,\pm S\times T]
$$
where $[u,v,w]$ is the matrix whose columns are vectors $u,v,w$. Since bases form invertible matrices, we have
$$
R=[S,T,\pm S\times T][s,t,s\times t]^{-1}
$$
where choosing $+$ will give a proper rotation and choosing $-$ will give an improper rotation.