I edited the answer because I found a counterexample to my reasoning. I am very sorry.
Let $X = Spec(k[x])$, $S = Spec(k)$ with the obvious map between spectra. I claim that $\mathcal{O} _{X} \otimes _{\pi^{-1} \mathcal{O} _{S}} \mathcal{O} _{X}$ cannot be quasi-coherent, at least if we equip it with the left action. (Or the right one, by the symmetry of the argument.)
Indeed, let $p = (x), q = (0)$ be points of $X$. We have isomorphisms
$(\mathcal{O} _{X} \otimes _{\pi^{-1} \mathcal{O} _{S}} \mathcal{O} _{X}) _{p} \simeq k[x] _{(p)} \otimes _{k} k[x] _{(p)} \simeq \bigoplus _{e_{i} \in I} k[x] _{(p)}$
of $k[x]$-modules, where $e_{i} \in I$ is some basis of $k[x] _{(p)}$ over $k$. (This is the basis of right summand, since we are using the left action.)
Assume by contradiction that $(\mathcal{O} _{X} \otimes _{\pi^{-1} \mathcal{O} _{S}} \mathcal{O} _{X})$ is quasi-coherent. Then the localization map
$((\mathcal{O} _{X} \otimes _{\pi^{-1} \mathcal{O} _{S}} \mathcal{O} _{X}) _{(p)} ) _{(q)} \rightarrow (\mathcal{O} _{X} \otimes _{\pi^{-1} \mathcal{O} _{S}} \mathcal{O} _{X}) _{(q)}$
would be an isomorphism. But
$((\mathcal{O} _{X} \otimes _{\pi^{-1} \mathcal{O} _{S}} \mathcal{O} _{X}) _{(p)}) _{(q)} \simeq (k[x] _{(p)} \otimes _{k} k[x] _{(p)}) _{(q)} \simeq (k[x] _{(p)}) _{(q)} \otimes _{k} k[x] _{p}$
and the localization map corresponds to the inclusion
$k[x] _{(q)} \otimes _{k} k[x] _{(p)} \hookrightarrow k[x] _{(q)} \otimes _{k} k[x] _{(q)}$
and this is not an isomorphism.