This is accomplished in different ways depending on what the Shinobi is doing. If the Shinobi is doing a ranged attack, then you will have to parry them to yank their chain and pull them to the ground. If it is a ranged guard break, then you have to counter guard break it, but note that the timing is different than a normal counter guard break and you cannot spam the gb button to counter. Instead you have to wait until the moment the chain lands on you and THEN you press the counter guard break button.
For an extensive guide on the Shinobi, you can check out my Shinobi guide thread on the forums here:
http://forums.ubi.com/showthread.php...-Shinobi-Guide