Put simply acupuncture works to help your body use its own healing mechanisms to help itself!
For example you have an injury, your body may produce natural cortisol to assist the healing process. Acupuncture can work on this mechanisms to promote more of this activity. Or instead of this you could get the synthetic version of this cortisone injected into your body. Both have very real mechanisms to assist you to recover. Personally I choose to let your body do the work for you.
Here is some more interesting research on acupuncture mechanisms.