To defeat Sanctus inside of Sparda in Mission 20, while Sanctus is airborne in his shield, get near and break it with sword attacks just like earlier in the game. However, he will sometimes block with the Sword of Sparda. When he does this, use the uppercut technique to break his guard. If you can, use the Devil Trigger while he is in the air to use a special combo and force him to the ground. If you fail to do the air combo, just let him fall to the ground. You may be able to get a few sword-based shots in, but do not try to rely on this as he may escape. At this point, use the uppercut in Devil Trigger form if possible. Afterward he will go back to being airborne again, in which case you should drop the Devil Trigger. After you have dropped his health down to about the 10% to 15% mark, he will use a charging sword attack (however, if you have perfected the aforementioned combo, you may bypass this). Defeating him requires precision. Time his charge towards you and uppercut to break his guard. Again, as soon as it is broken, get into the Devil Trigger uppercut and finish him off. During the second battle against Sanctus as the False Prophet, timing is once again vital. All you must do is uppercut his attacks away.
An easy way to drop Sanctus' Shield during either of his encounters, have a full Exceed gauge (Ex-act or Max-act helps), then approach Sanctus, jump, and perform an Ex Calibur. If the full combo hits, his shield will be down. You can now proceed to make him fully vulnerable to attack using the above method, or however desired.