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Our eyes are actually extremely sensitive. When adjusted for complete darkness, it takes just two or three individual photons hitting a light-sensitive cell in the eye within a short period to fire off the corresponding neurons and be detected as a light.
When you're trying to see in very low light, do you notice how your vision looks a bit grainy, almost like there's a subtle bit of static? That's individual light-sensitive cells going off in your eyes, one at a time, each one triggered by only a few photons each. When there are so few photons coming into your eyes, there aren't enough to hit and trigger every single cell, so you get individual cells flashing on and off, causing this grainy/static texture.
Given the way eyes work, though, I'm not sure you'll ever find a pulse brief enough to be imperceptible. Our eyes have kind of a built-in afterglow effect -- if there are enough photons hitting the retina cells, no matter how brief the pulse, the cells will be triggered, and you will perceive a flash of light. The perceived duration of the flash will probably be much, much longer than the actual flash, as your cells aren't able to turn off as quickly as the light source might be able to.
When you're talking about just a handful of individual photons, 'intensity' becomes less meaningful. The only way to make those few photons more intense would be to increase their frequency to something more energetic ... but once you get into ultraviolet frequencies and beyond, they will be outside the range of human perception anyway.