One of the main reasons is that despite the level of destruction the fire was actually very slow burning. The mayor of London was awoken when it first broke out but promptly went back to bed declaring "A woman might piss it out." Which gives a clear indication that it was hardly the great conflagration people commonly think of.

However the total lack of a unified metropolitan emergency service and the prevalence of wooden and thatch construction meant that it was never fully brought under control.

I'm on mobile right now but when I get home I'll try and link to a couple of sources and give you an exact timeline but I believe that it actually burned for three days, moving slowly across the city.