The physiological signs of pain occur mostly as a consequence of the way we consciously experience and process pain. (This is why "general anesthetic" works: central processing of pain is required before sensory input is actually registered as painful, and so, without the brain there to decide that a thing is painful, the physiological consequences don't happen. Pain that would give you a heart attack if you were awake doesn't cause the slightest physiological problem when you're unconscious from general anesthesia.)

If you are receiving a lot of "painful-stimulus describing" sensory input, and you're consciously experiencing those stimuli as painful qualia—but your body shows relatively little physiological response—then you have a high tolerance for pain.

This can be measured by using a standardized painful stimulus (e.g. a sub-cutaneous injection of a standardized dose of some insect's venom) together with an fMRI (or just self-reporting) to measure the intensity of the painful qualia, and various physiological monitors (EKG, etc.) to measure physiological response to the pain.

I believe this has been done before specifically in the case of certain sects of monks who like to demonstrate the depth of their meditative ability by tolerating large amounts of pain. They did the experiment to try to figure out whether the monks are tolerating an experienced pain, or merely are somehow not experiencing the painful stimulus as pain-qualia.