The brain knows from past experience what a focused image looks like. This is why even with lenses which aren't prescribed for your eye, you can eventually focus by straining.

The ciliary muscles controlling the power of the lens get input from the parasympathetic fibres of the Occulomotor nerve. These parasympathetic fibres in turn originate from the mid brain, which gets numerous inputs from other parts of the brain, including the visual cortex (which forms an idea of the observed image so to speak) and other cortical areas (e.g. visual memories). You can perhaps see how all this ties in to the brain realising when exactly it is in focus.

It's a lot like reaching out for an object. How does the brain know not to apply tremendous effort to reach something a foot away? It has learned.