During the scene, the intense experiences of both pain and pleasure trigger a sympathetic nervous system response, which causes a release of epinephrine from the suprarenal glands, as well as a dump of endorphins and enkephalins. These natural chemicals, part of the fight or flight response, produce the same effect as a morphine-like drug, increasing the pain tolerance of the submissive as the scene becomes more intense. Since the increase of hormones and chemicals produces a sort of trance-like state, the submissive starts to feel out-of-body, detached from reality, and as the high comes down, and the parasympathetic nervous system kicks in, a deep exhaustion, as well as incoherence. Many submissives, upon reaching a height of subspace, will lose all sensation of pain, as any stimulus causes the period to prolong.
I can't speak for the science of it. Anyway, I prefer Clarisse Thorn's description, and I feel great about quoting from it heavily: