When confusion is to hit you, Magic guard negates damage. BUT will magic guard stop confusion from even working? I never have seen a Pokemon "hit itself" in confusion when it's ability is Magic guard. So I was wondering if Magic guard was just an OP "Own Tempo" :D
No, Magic Guard does not prevent the effects of confusion.
>Damage from confusion still occurs.
Only Own Tempo exclusively prevents confusion as an ability. Any Pokemon that's confused only has a chance of hitting itself, so you were just lucky not to have a Pokemon with Magic Guard hit itself when confused.
Bulbapedia lists what Magic Guard prevents.