There are tons of reasoning you can do to deduce that he does have it.Can you prove that he does have it with a viz scan?
1. He has Itachi's eyes, which contain Tsukiyomi
2. Danzo compared the Genjutsu he has used on him specifically with Tsukiyomi. This is key to explain: Why would Danzo compare a technique Sasuke used to Tsukiyomi's ability to control time perception in order to some up the quality of the Genjutsu, when Tsukiyomi is the only technique that has been shown to control time perception? Let's say for example, you are looking at the quality of a car. Would you say "This car is pretty good, but isn't THAT good because it can't travel on water like that boat over there?" No, because summing up the quality of something with a trait that is impossible for it to possess would be brain-dead. Why mention the time-controlling aspect of Tsukiyomi if the technique Sasuke used WASN'T Tsukiyomi? Why compare it all to Tsukiyomi if it wasn't Tsukiyomi, especially when Itachi has far more well-known Genjutsu to compare it to? It's not like it was just for the sake of riling Sasuke up via psychological warfare, as just saying "You're not as good as Itachi" or "Itachi has even better Genjutsu than this" would suffice.
3. Sasuke has Amaterasu in his left eye. As shown with Itachi, Amaterasu and Tsukiyomi are held in opposite eyes. Tie this in with the fact that Sasuke used a Genjutsu with his right Mangekyo that flipped the color scale, something only Tsukiyomi has been shown to do, you can surmise that it was Tsukiyomi, but just very weak.
Not everything will be spoon-fed to you, you have to look at smaller hints and details to complete the big picture.
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