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Itachi can't cast gaara in genjutsu through his 3rd eye.. Gaara's 3rd eye is a jutsu, so it couldn't affect gaara nor it can affect his chakra flow but maybe it would cancel gaara's technique..
But from what i read from the other member/s, gaara's 3rd eye is likely connected via chakra, so itachi's genjutsu can still mess up his chakra flow. But How..? does gaara's 3rd eye has some kind of a chakra string that connected to gaara himself.? and itachi's genjutsu will just running into the chakra string and goes directly to gaara's chakra system..? it doesn't make any sense.. Gaara's 3rd eye is a jutsu that made up of sand, so even if the uchiha's sharingan will likely to put that into genjutsu, but then again, it will never affect on gaara's chakra flow..
---------- Post added at 02:18 PM ---------- Previous post was at 02:10 PM ----------
But let's say he will use a genjutsu using eye contact and Gaara will use his third eye...
The third eye is connected to Gaara's brain, we know that from the Chuunin Exam, so it works exactly like a normal eye...the connection is via chakra, that's the only possible way...so if there is an eye regardless if it's sand or not, and it is connected to Gaara...then Gaara will be caught in a genjutsu...
But this is not that important though, because Itachi doesn't need eye contact to perform genjutsu so...