First, the use of the term 'sterile' is going to catch flack. Those bottles have probably never been sterile. However, sanitary is what you are aiming for.
Second, some folks will point out that water bottles may not be strong eough fo rthe levels of carbonation that beer typically reaches.
Third, some folks will say that PET bottles are not good for long term beer storage.
Finally, yes if you pour out the water and then immediately recap them, you are in possession of a sanitary vessel. (I am assuming this is commercial water purchased in the US) Regulations surrounding bottled water production require that bottled water be sanitary and bottled under sanitary conditions.