Tsukuyomi is a genjutsu, it not something standard, it depends on how the user wants to use it. Sasuke has it, and the only problem is that he doesn't have complete control over it, unlike Itachi.
Put it another way: Sasuke has more control over Amaterasu (he did create/learn/get Blaze release) which is something Itachi doesn't have even though he has Amaterasu. And Itachi on the other hand is more proficient with genjutsu, so much that he can actually control time within his tsukuyomi, Something Sasuke can't do, he also can't keep it active for a long period.
So just because he doesn't use it so often (it doesn't suit his style, he was never a genjutsu fighter to begin with, unlike Itachi who uses it on a regualr basis) doesn't mean he doesn't have it.
Proof:
1.Since he got MS all the genjutsu he used were MS genjutsus, never once did he use a genjutsu with the regular sharingan.
2.His eye bleeds whenever he uses Genjutsu.
3.It says clearly in the aatabook (written by Kishi) that in order to use Susanoo one must have both Tsukuyomi and Amaterasu. (sorry i don't have the link to the page, but i hope someone comes who actually has it)
And just where does it say in the Manga that Tsukuyomi controls time? Yea Itachi can do it, but there is no proof that it is something standard. Itachi can do it because he is a genjutsu master, and using it so many time, as his basic fighting style it is only normal for him to be proficient with it.