Yup. Chlorine/chloramine in the water is what kills the bacteria. Also if the temperature difference between the water in the aquarium and the water coming out of the tap is extreme, say 30 or 40 degrees, that would also likely kill off a small amount of the bacteria too. 

I usually refill my canister filters with pretreated tap water like you did  and never had a spike in ammonia or nitrite, so you should be fine (been doing it this way for years).  I add a little more conditioner/dechlorinator than the recommended dose when i'm using the water to refill the canister filters, just to make sure all the chlorine get neutralized quickly.