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Like Kyubi explains here, Minato was so skilled in chakra control that he could even mold his chakra to match the one he decides to transfer his chakra in(in this case, it was Naruto):
We know how genjutsu works. It is created when a ninja extends their chakra flow through the cerebral nervous system of their opponent to control their mind, thereby affecting their five senses
So since Minato can alter his chakra to match someone else's chakra, all what he needs when he is under a genjutsu, is to change his chakra flow into the opponent's one so that when the opponent would try to take control of his chakra flow by extending his own in Minato's, it would not only have zero effect on him at all, but could even conserve/gain the chakra implemented in him and make it his own
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We know how genjutsu works. It is created when a ninja extends their chakra flow through the cerebral nervous system of their opponent to control their mind, thereby affecting their five senses
So since Minato can alter his chakra to match someone else's chakra, all what he needs when he is under a genjutsu, is to change his chakra flow into the opponent's one so that when the opponent would try to take control of his chakra flow by extending his own in Minato's, it would not only have zero effect on him at all, but could even conserve/gain the chakra implemented in him and make it his own
