You forget what happen during/after the kage summit. Zetsu gave him the chakra reserves of all 5kages+their bodyguards and Karin healed him in Tobi's dimension. So it's safe to assume that he was perfectly well while fighting Danzo. He was even stronger since he got more chakra(thanks to Zetsu) and was able to upgrade his Susanoo(he only had ribcage during kage summit). And again during/after his fight against Danzo, he got healed by Karin, but maybe he wasn't 100% fit though, but he was healed, and was able to upgrade his Susanoo again creating a form that he couldn't even do at 100% against Danzo, but got blind after that.
Yes Susanoo is strong, but like we've seen against Gaara, it has weaknesses. You can attack it from underground and Kakashi can do it by using doton like i've said on my first post. By hiding underground he has also nothing to fear about arrows or Amaterasu, etc