Board Thread:Versus Debates/@comment-26369695-20151019153851/@comment-26537507-20151027140344

Kabuto didn't fight by sensing chakra. Here's a quote from his page under the Snake Techniques heading: To counteract genjutsu that are dependent upon eye contact, Kabuto can rely solely upon his snakes' ability to perceive their surroundings through sensing the ambient temperatures and smells using their tongues, rather than his own sight.

In most cases basic Sharingan genjutsu would be useless, but having Shisui in this fight changes things. Proficient Sharingan users struggled to get out of even his most basic genjutsu, to the point where Danzo was forced to use Izanagi to get out of one. For Itachi, eye contact is only required for Tsukuyomi, so he could easily trap either Naruto of Sasuke for a few seconds (before they break out). Shisui was reported to be able to trap many individuals over great distances, so putting both Naruto and Sasuke in a genjutsu, which could take them a little longer to break out.