We do not need the integral assumption:
Take $0 \
eq f \in I$. We have $\phi(rf)=0 \in S$, hence $rf \in T$ for all $r \in R$. In particular $f \in T$. Now we have $r = \frac{rf}{f} \in Quot(T)$, which shows $R \subset Quot(T)$, which is literally all we need.