Susano'o in cases is awakened with the Mangekyo Sharingan. The awakening of the MS causes "special chakra" to "sprout" in the brain of an Uchiha. Now, because Itachi could use Susano'o whilst blind, and Madara without eyes, I think that it's safe to conclude that the chakra that "sprouts" in the brain is for Susano'o. Just because his EMS mutated and awakened into the Rinnegan, doesn't mean that he lost the chakra which "sprouted" in his brain at the time of awakening MS.
It's been stated that his eyes weren't a Sharingan anymore, but Rinnegan. It's more than likely that changing between Sharingan and Rinnegan was only doable whilst an Edo. The Edo Tensei eyes were not the real thing, after all.