Actually, this sort of injury is a result of Newton's First Law rather than the Third Law. Because your body is restrained by your harness, it decelerates with the seat (which presumably remains attached to the frame of the vehicle), whereas your unrestrained head tends to continue moving in the same direction and at the same speed as the vehicle until the structures of your neck begin to provide resistance to bring it to a stop.
What is interesting about recent high speed imagery of rear-end collisions is that the cervical spine experiences both hyperextension (in the lower vertebrae) and hyperextension (in the upper vertebrae), which probably causes the soft tissue damage that causes the pain and injury associated with whiplash.
Again, whiplash is acceleration injury, not deceleration injury. (You can actually suffer a whiplash injury from a collision with a barrier in front of you AS A RESULT OF A HEADREST: after the initial forward motion of your head, you may "bounce back" and hit the headrest hard enough (about a 10G impact) to produce a secondary deceleration injury (and whiplash).
The best method to prevent such injuries is the neck restraint worn by race car drivers. However, few pax and even fewer pilots are likely to adopt their use. ;-)
-- Chris