No, he didn't. Aside from anything else, the “Commander in Chief” role is solely commanding the military under the laws prescribed by Congress. Public diplomatic threats (even threats that, were they carried through, would involve acting in the C-in-C role) are not part of that role.

Syrian President Bashar al-Assad should heed U.S. warnings to neither use nor move chemical or biological weapons, lest he risk crossing a "red line" and provoke a U.S. military response, President Barack Obama said Monday.