Hmm...
Well you remember how powerful Naruto and Sasuke got when they got the chakra from Hagoromo? Or how much more powerful Madara and Obito got when taking in the Juubi's chakra? Like that. His chakra was potent enough to utilize the "Perfect Susano'o" without needing an EMS. The manga always stipulated that getting the EMS was basically like intertwining the donee and the person's eyes who's being transplanted. Remember, when Sasuke first implanted Itachi's eyes, he said that he felt Itachi's power flowing through him. It's like a harmonization of the two brothers chakra making their chakra more powerful and letting Sasuke (and by extension Madara, who did it first), access the highest form of Susano'o. Stronger chakra = Higher form of Susano'o. Indra descended from Hagoromo directly and thus has very powerful chakra.