Minato wins this one, Minato and Itachi are the two most intelligent shinobi in Naruto. I would expect Minato to know a lot about the sharingan as he believed that Obito was Madara. He must have made a lot of research on who Madara is and what jutsu's he posses, meaning he may know about the Susano'o and or Amateratsu. This would give him a large advantage in the fight as he would have had prep time and would have been able to plan some situations during the battle if a MS user were to use his Susano'o or Amateratsu. However even if he didn't know anything about them, he has showed to be able to analyze techniques in great detail with only one use, such as Kakashi's chidori, and has been able to create the rasengan using his observational skills by watching the Kyuubi make a TBB. Minato also has an amazing offense which is combined with his FTG making him almost invincible.
Minato also has shown to have a great offense which is combined with his FTG making him almost invincible. His normal Rasengan is supposedly the size of a big ball Rasengan meaning it may be a one shot technique. Minato has large chakra reserves considering the fact he can summon Gamabunta, or use him in the technique; Food cart destroyer. If Minato where to use Food cart destroyer on a full sized Kurama and and pin him down for a decent amount of time, it should easily be able to flatten a complete Susano'o.
Now if Itachi were to turn on his complete Susano'o and use Yasaka Magatama, then Minato should easily be able to create a space-time barrier and teleport it to one of his FTG kunai's which have been dispersed on the floor, or throw a FTG kunai and make the Magatama teleport to that kunai. This means the only thing Itachi would be capable of doing is putting Minato under Genjutsu or using Amateratsu, which would be on a huge disadvantage against someone who is constantly on the move like Minato.
If Itachi got the slightest opportunity to use Genjutsu, than he would definitely use it. Putting Minato under Genjustu such as the one he used on Naruto would be easily blocked by Minato with Genjutsu Kai within seconds, as Genjutsu Kai takes good chakra control, and judging from his Rasengan and him being Hokage his chakra control must be great. On the other hand if Itachi where to use Tsukoyomi Minato would be finished, but he will not use Tsukoyomi as easily as people would expect him to. Someone who may FTG at any moment puts someone like Itachi with extremely low chakra reserves and stamina at a huge risk of using any jutsu ineffectively let alone Tsyukoyomi (as well as amateratsu), something which takes large amounts of chakra if it hits or misses, which is a 50/50 chance.
