Lincoln issued the Proclamation under his authority as "Commander in Chief of the Army and Navy" under Article II, section 2 of the United States Constitution.[3] As such, he had the martial power to suspend civil law in those states which were in rebellion. He did not have Commander-in-Chief authority over the four slave-holding states that had not seceded: Missouri, Kentucky, Maryland and Delaware. The Emancipation Proclamation was never challenged in court. To ensure the abolition of slavery everywhere in the U.S., Lincoln pushed for passage of the Thirteenth Amendment. Congress passed it by the necessary 2/3 vote in February 1865 and it was ratified by the states by December 1865.[4]
Note that the Emancipation Proclamation was a war-time effort, and only applied to states that were in rebellion against the Union, and thus did not apply to all the slaveholding states.
As far as I know, there are currently no US states in open armed rebellion against the United States, and thus the President has no CIC justification to invoke.