The classic way is genjutsu training. A ninja can learn to recognize and cancel genjutsu by disturbing their own chakra network, which the genjutsu controls. If not a teammate is required to release the genjutsu. Fundamentally, a weak genjutsu can be broken easily by a strong ninja, as such, dangerously strong genjutsu are more difficult to evade and release, such as Tsukuyomi. Tailed Beasts and Jinchuriki have an advantage in this regard, as a perfect jinchuriki can have their Tailed Beast release the genjutsu as soon as it is administered, and so it makes genjutsu impossible to use. Jiraiya also said, that if you cannot use genjutsu, then you should learn to cancel it, to remove it from the fight period. For more info, see Genjutsu.