-Near the exploded Mako site is a small forest. Wonder around in it until you fight a ninja woman. After defeating her, there will be a save point; don't use it or she will run away. Speak with her and tell her you don't want to fight her again. Then, tell her you're terrified of her. When she asks if you need her help, say "Yes" then tell her that you're leaving and don't ask for her name.
-Alternatively, equip the Enemy Away Materia, which is won in the Gold Saucer Chocobo Racing, and a Luck Plus Materia. Go into any forests and wait for a while. Note that the Enemy Away Materia must be at Master Level for a higher percentage of chance to encounter Yuffie.