We know among Sasuke's arsenal, he now holds all of Itachi's dojutsu. Right now, he can only cast Amaterasu in response to Madara activating the sharingan in closer quarters. But, the fact that he still has all of Itachi's dojutsu, means that in the future, he may be able to individually cast them when needed.
Right now it appears that Sasuke has gained a further step ahead of Naruto just by having Amaterasu. But is it possible that Naruto already posses an ultimate counter to that devastating eye technique?
Even though Amaterasu is known to burn for seven days and seven nights and continue to burn until its victim is consumed in its direct view, could it be possible that it can't burn through a certain substance?
Naruto holds two types of chakra. The red chakra belonging to the Kyuubi, has an incredible defense against all sorts of attacks. The down side is that with extensive usages of the tailed states, Naruto suffers damage over repeated healing due to the burning chakra, which results in accelerated growth of cells and eventual shortened life span.
But perhaps if Naruto taps into the cloak just briefly, he can make great use of his defensive abilities without causing too much or any damage to himself. Even the first tailed State's chakra was enough to make short work of Sasuke's fire elemental ninjutsu.
Of course the Amaterasu is much stronger than some C-B rank fire elemental ninjutsu, but the 4th tailed state's chakra was strong enough to even ward off Orochimaru's Kusanagi blade.
Of course that hardly tells us anything, but it just helps me prove that the Amaterasu may not be getting inside Naruto's body so easily.
We understand that Naruto will probably not rely on the 4th tailed state, but since he's getting the key to his seal, all of the Kyuubi power bestowed to him will be released, thus he'll obtain a great amount of powerful chakra for full use. Obviously he'll have to master it so he does not go into the tailed states, but with the mastery, perhaps he can put up his own shield to ward himself of that powerful fire.
We also know that the Kyuubi's chakra makes the air thick and fills it with malice, much like Amaterasu. The Kyuubi's chakra can even burn to a great extent if thrown in the direction of an opponent. The chakra can also level mountains and clear landscapes when concentrated.
Brute power like that, may even blow the Amaterasu away.
Now we know Sasuke's sharingan can suppress Kyuubi's chakra, but can he stop Naruto from diving into that chakra? I doubt it. I believe the only thing Sasuke can do with the sharingan is keep the Kyuubi from helping Naruto. With further mastery of the Kyuubi's chakra, Naruto can help himself. Remember that chakra is in his system, he can draw it out by focusing.
This is just my thought about Naruto standing up to the Amaterasu.