who says he didn't use susanoo
it was the end of the fight and it was said that they fought all through the night so even if ps doesn't cause any strain on the body it still takes some chakra to use it and i doubt madara could keep it up that long
in other words madara probably just didn't have enough chakra at the end of the fight the showed in the anime to keep up susanoo in the end of the fight(we only saw the end of the fight)