No, this is not true.
Denote by $S=k[X_0,...,X_n]$, $X$ a hypersurface in $\mathbb{P}^n$ defined by an equation $F$ of degree $d$. Then there is an injective morphism $S(-d) \to S$ given by multiplication by $F$. But the induced morphism $(S/(F))(-d) \to S/(F)$ is not injective.
Applying the associated coherent sheaf functor to the modules give a counterexample.